In [1]:
#Setup the working environment
setwd("/hpc/group/pbenfeylab/mz187/")
In [2]:
# Load the basic package_Seurat
suppressMessages(library(tidyverse))
suppressMessages(library(Seurat))
suppressMessages(library(cowplot))
suppressMessages(library(ComplexHeatmap))
suppressMessages(library(circlize))
suppressMessages(library(GeneOverlap))
suppressMessages(library(gprofiler2))
suppressMessages(library(ggrepel))
suppressMessages(library(muscat))
suppressMessages(library(limma))
suppressMessages(library(scran))
suppressMessages(library(future))
suppressMessages(library(RColorBrewer))

Warning message:
“package ‘tidyverse’ was built under R version 4.2.3”
Warning message:
“package ‘tibble’ was built under R version 4.2.3”
Warning message:
“package ‘tidyr’ was built under R version 4.2.3”
Warning message:
“package ‘readr’ was built under R version 4.2.3”
Warning message:
“package ‘purrr’ was built under R version 4.2.3”
Warning message:
“package ‘dplyr’ was built under R version 4.2.3”
Warning message:
“package ‘stringr’ was built under R version 4.2.3”
Warning message:
“package ‘forcats’ was built under R version 4.2.3”
Warning message:
“package ‘lubridate’ was built under R version 4.2.3”
Warning message:
“package ‘ComplexHeatmap’ was built under R version 4.2.1”
Warning message:
“package ‘circlize’ was built under R version 4.2.3”
Warning message:
“package ‘GeneOverlap’ was built under R version 4.2.1”
Warning message:
“package ‘gprofiler2’ was built under R version 4.2.3”
Warning message:
“package ‘muscat’ was built under R version 4.2.2”
Warning message:
“package ‘limma’ was built under R version 4.2.3”
Warning message:
“package ‘scran’ was built under R version 4.2.3”
Warning message:
“package ‘SingleCellExperiment’ was built under R version 4.2.2”
Warning message:
“package ‘SummarizedExperiment’ was built under R version 4.2.2”
Warning message:
“package ‘MatrixGenerics’ was built under R version 4.2.1”
Warning message:
“package ‘matrixStats’ was built under R version 4.2.3”
Warning message:
“package ‘GenomicRanges’ was built under R version 4.2.3”
Warning message:
“package ‘BiocGenerics’ was built under R version 4.2.1”
Warning message:
“package ‘S4Vectors’ was built under R version 4.2.3”
Warning message:
“package ‘IRanges’ was built under R version 4.2.3”
Warning message:
“package ‘GenomeInfoDb’ was built under R version 4.2.3”
Warning message:
“package ‘Biobase’ was built under R version 4.2.3”
Warning message:
“package ‘scuttle’ was built under R version 4.2.3”
Warning message:
“package ‘RColorBrewer’ was built under R version 4.2.3”
In [3]:
# Read integrated Copilot project
rc.integrated <- readRDS("Rice_8S_snRNA-seq_seu3_filtered-102824.rds")
In [4]:
# Find included samples
table(rc.integrated$orig.ident)

sc_295 sc_296 sc_297 sc_298 sc_299 sc_300 sc_301 sc_302 
  2314   4264   9173   7046   6926   6912   9593   8797

Re-annoate all the cell types¶

In [5]:
# Check the seurat clusters for the integrated object
options(repr.plot.width=16, repr.plot.height=16)
DimPlot(rc.integrated, reduction = "umap", group.by = "seurat_clusters", label = T)

Warning message:
“Using `as.character()` on a quosure is deprecated as of rlang 0.3.0. Please use `as_label()` or `as_name()` instead.
This warning is displayed once every 8 hours.”
In [6]:
# Assign cell type annotation to the clusters
rc.integrated$manual.anno <- as.character(rc.integrated$seurat_clusters)
rc.integrated$manual.anno[which(rc.integrated$seurat_clusters=='0')] <- "Meristem"
rc.integrated$manual.anno[which(rc.integrated$seurat_clusters=='1')] <- "Exodermis"
rc.integrated$manual.anno[which(rc.integrated$seurat_clusters=='2')] <- "Meristem"
rc.integrated$manual.anno[which(rc.integrated$seurat_clusters=='3')] <- "Meristem"
rc.integrated$manual.anno[which(rc.integrated$seurat_clusters=='4')] <- "Exodermis"
rc.integrated$manual.anno[which(rc.integrated$seurat_clusters=='5')] <- "Pericycle"
rc.integrated$manual.anno[which(rc.integrated$seurat_clusters=='6')] <- "Meristem"
rc.integrated$manual.anno[which(rc.integrated$seurat_clusters=='7')] <- "Meristem"
rc.integrated$manual.anno[which(rc.integrated$seurat_clusters=='8')] <- "Cortex"
rc.integrated$manual.anno[which(rc.integrated$seurat_clusters=='9')] <- "Meristem"
rc.integrated$manual.anno[which(rc.integrated$seurat_clusters=='10')] <- "Mature root cells"
rc.integrated$manual.anno[which(rc.integrated$seurat_clusters=='11')] <- "Trichoblast"
rc.integrated$manual.anno[which(rc.integrated$seurat_clusters=='12')] <- "Xylem"
rc.integrated$manual.anno[which(rc.integrated$seurat_clusters=='13')] <- "Meristem"
rc.integrated$manual.anno[which(rc.integrated$seurat_clusters=='14')] <- "Xylem"
rc.integrated$manual.anno[which(rc.integrated$seurat_clusters=='15')] <- "Exodermis"
rc.integrated$manual.anno[which(rc.integrated$seurat_clusters=='16')] <- "Pericycle"
rc.integrated$manual.anno[which(rc.integrated$seurat_clusters=='17')] <- "Pericycle"
rc.integrated$manual.anno[which(rc.integrated$seurat_clusters=='18')] <- "Meristem"
rc.integrated$manual.anno[which(rc.integrated$seurat_clusters=='19')] <- "Atrichoblast"
rc.integrated$manual.anno[which(rc.integrated$seurat_clusters=='20')] <- "Meristem"
rc.integrated$manual.anno[which(rc.integrated$seurat_clusters=='21')] <- "Sclerenchyma"
rc.integrated$manual.anno[which(rc.integrated$seurat_clusters=='22')] <- "Sclerenchyma"
rc.integrated$manual.anno[which(rc.integrated$seurat_clusters=='23')] <- "Atrichoblast"
rc.integrated$manual.anno[which(rc.integrated$seurat_clusters=='24')] <- "Phloem"
rc.integrated$manual.anno[which(rc.integrated$seurat_clusters=='25')] <- "Atrichoblast"
rc.integrated$manual.anno[which(rc.integrated$seurat_clusters=='26')] <- "Exodermis"
rc.integrated$manual.anno[which(rc.integrated$seurat_clusters=='27')] <- "Meristem"
rc.integrated$manual.anno[which(rc.integrated$seurat_clusters=='28')] <- "Meristem"
rc.integrated$manual.anno[which(rc.integrated$seurat_clusters=='29')] <- "Pericycle"
rc.integrated$manual.anno[which(rc.integrated$seurat_clusters=='30')] <- "Mature root cells"
rc.integrated$manual.anno[which(rc.integrated$seurat_clusters=='31')] <- "Xylem"
rc.integrated$manual.anno[which(rc.integrated$seurat_clusters=='32')] <- "Trichoblast"
rc.integrated$manual.anno[which(rc.integrated$seurat_clusters=='33')] <- "Pericycle"
rc.integrated$manual.anno[which(rc.integrated$seurat_clusters=='34')] <- "Pericycle"
rc.integrated$manual.anno[which(rc.integrated$seurat_clusters=='35')] <- "Meristem"
rc.integrated$manual.anno[which(rc.integrated$seurat_clusters=='36')] <- "Pericycle"
rc.integrated$manual.anno[which(rc.integrated$seurat_clusters=='37')] <- "Phloem"
rc.integrated$manual.anno[which(rc.integrated$seurat_clusters=='38')] <- "Atrichoblast"
rc.integrated$manual.anno[which(rc.integrated$seurat_clusters=='39')] <- "Endodermis"
rc.integrated$manual.anno[which(rc.integrated$seurat_clusters=='40')] <- "Trichoblast"
rc.integrated$manual.anno[which(rc.integrated$seurat_clusters=='41')] <- "Pericycle"
rc.integrated$manual.anno[which(rc.integrated$seurat_clusters=='42')] <- "Endodermis"
rc.integrated$manual.anno[which(rc.integrated$seurat_clusters=='43')] <- "Phloem"
rc.integrated$manual.anno[which(rc.integrated$seurat_clusters=='44')] <- "Trichoblast"
rc.integrated$manual.anno[which(rc.integrated$seurat_clusters=='45')] <- "Meristem"
rc.integrated$manual.anno[which(rc.integrated$seurat_clusters=='46')] <- "Sclerenchyma"
rc.integrated$manual.anno[which(rc.integrated$seurat_clusters=='47')] <- "Exodermis"
rc.integrated$manual.anno[which(rc.integrated$seurat_clusters=='48')] <- "Meristem"
rc.integrated$manual.anno[which(rc.integrated$seurat_clusters=='49')] <- "Pericycle"
rc.integrated$manual.anno[which(rc.integrated$seurat_clusters=='50')] <- "Pericycle"
rc.integrated$manual.anno[which(rc.integrated$seurat_clusters=='51')] <- "Meristem"
rc.integrated$manual.anno[which(rc.integrated$seurat_clusters=='52')] <- "Trichoblast"
rc.integrated$manual.anno[which(rc.integrated$seurat_clusters=='53')] <- "Xylem"
rc.integrated$manual.anno[which(rc.integrated$seurat_clusters=='54')] <- "Phloem"
rc.integrated$manual.anno[which(rc.integrated$seurat_clusters=='55')] <- "Phloem"
In [7]:
table (rc.integrated$manual.anno)

     Atrichoblast            Cortex        Endodermis         Exodermis 
             4022              1520              1255              6392 
Mature root cells          Meristem         Pericycle            Phloem 
             2294             17739              8669              2662 
     Sclerenchyma       Trichoblast             Xylem 
             2808              3804              3860
In [8]:
# Make final cell type annotation figure
order <- c("Meristem", "Atrichoblast", "Trichoblast", "Exodermis","Sclerenchyma","Cortex", "Endodermis","Pericycle", "Phloem", "Xylem","Mature root cells")
palette <- c("#360167","#59adf6", "#Ff4061", "#F8f38d", "#32CD32", "#BF40BF", "#Ffb480","#08cad1", "#9d94ff","#834200","#b7bcc0")
rc.integrated$manual.anno <- factor(rc.integrated$manual.anno, levels = order[sort(match(unique(rc.integrated$manual.anno),order))]) 
color <- palette[sort(match(unique(rc.integrated$manual.anno),order))]
options(repr.plot.width=12, repr.plot.height=12)
DimPlot(rc.integrated, reduction = "umap", group.by = "manual.anno", cols= palette, pt.size = 0.1)+ggtitle("Celltype Annotation UMAP")
In [9]:
## Subgroup the "normal" groups for the following analysis
rc.kitaake <- subset(rc.integrated, cells=colnames(rc.integrated)[which(rc.integrated$condition!="X.K")])
In [10]:
table(rc.kitaake$gel_soil)

non-compact soil     compact soil              gel 
           13838            18390            16219

Subgroup the "normal" conditions: normal gel conditions and normal soil conditions (non-compacted soils)¶

In [11]:
table(rc.kitaake$gel_soil, rc.kitaake$orig.ident)

                  
                   sc_297 sc_298 sc_299 sc_300 sc_301 sc_302
  non-compact soil      0      0   6926   6912      0      0
  compact soil          0      0      0      0   9593   8797
  gel                9173   7046      0      0      0      0
In [12]:
## Subgroup the "normal" groups for the following analysis
rc.comparison <- subset(rc.kitaake, cells=colnames(rc.kitaake)[which(rc.kitaake$gel_soil!="non-compact soil")])
In [71]:
# Define the datasets used for Gel VS Soil comparison
rc.comparison$normal <- rc.comparison$orig.ident %in% c("sc_297","sc_298")

rc.comparison$normal <- as.character(rc.comparison$normal)

rc.comparison$normal <- gsub("TRUE", "gel", rc.comparison$normal,
                               ignore.case = FALSE, perl = FALSE,
                               fixed = T, useBytes = FALSE)

rc.comparison$normal <- gsub("FALSE", "soil", rc.comparison$normal,
                               ignore.case = FALSE, perl = FALSE,
                               fixed = T, useBytes = FALSE)

rc.comparison$normal <- factor(rc.comparison$normal , 
                                 levels=c("gel", "soil"))

table(rc.comparison$normal, rc.comparison$orig.ident)

      
       sc_297 sc_298 sc_301 sc_302
  gel    9173   7046      0      0
  soil      0      0   9593   8797
In [72]:
table(rc.comparison$normal, rc.comparison$manual.anno)

      
       Meristem Atrichoblast Trichoblast Exodermis Sclerenchyma Cortex
  gel      8540          624         646      1701          788    171
  soil     3148         2218        1505      2051          936    776
      
       Endodermis Pericycle Phloem Xylem Mature root cells
  gel         381      2075    142  1076                75
  soil        238      3316   1212  1936              1054
In [ ]:

DE analysis with Muscat package¶

In [73]:
# construct sce manually
my_metadata <- data.frame(sample_id = rc.comparison$orig.ident,
group_id = rc.comparison$normal,
cluster_id = rc.comparison$manual.anno)
head(my_metadata)
sce <- SingleCellExperiment(assays = list(counts = rc.comparison@assays$RNA@counts),
colData = my_metadata)
sce
(sce <- prepSCE(sce,
kid = "cluster_id", # subpopulation assignments
gid = "group_id", # group IDs (ctrl/stim)
sid = "sample_id", # sample IDs (ctrl/stim.1234)
drop = TRUE)) # drop all other colData columns
A data.frame: 6 × 3
sample_idgroup_idcluster_id
<chr><fct><fct>
AAACCCAAGATGAATC_1sc_297gelExodermis
AAACCCAAGGACGCTA_1sc_297gelPericycle
AAACCCAAGGATATGT_1sc_297gelAtrichoblast
AAACCCAAGGCACCAA_1sc_297gelCortex
AAACCCAAGTCCCTAA_1sc_297gelExodermis
AAACCCACAACCCGCA_1sc_297gelMeristem 
class: SingleCellExperiment 
dim: 41204 34609 
metadata(0):
assays(1): counts
rownames(41204): LOC-Os01g01010 LOC-Os01g01019 ... LOC-Os09g27120
  LOC-Os09g39170
rowData names(0):
colnames(34609): AAACCCAAGATGAATC_1 AAACCCAAGGACGCTA_1 ...
  TTTGTTGTCTCGGTCT_8 TTTGTTGTCTGATTCT_8
colData names(3): sample_id group_id cluster_id
reducedDimNames(0):
mainExpName: NULL
altExpNames(0):
class: SingleCellExperiment 
dim: 41204 34609 
metadata(1): experiment_info
assays(1): counts
rownames(41204): LOC-Os01g01010 LOC-Os01g01019 ... LOC-Os09g27120
  LOC-Os09g39170
rowData names(0):
colnames(34609): AAACCCAAGATGAATC_1 AAACCCAAGGACGCTA_1 ...
  TTTGTTGTCTCGGTCT_8 TTTGTTGTCTGATTCT_8
colData names(3): cluster_id sample_id group_id
reducedDimNames(0):
mainExpName: NULL
altExpNames(0):
In [74]:
# Store cluster and sample IDs, as well as the number of clusters
# and samples into the following simple variables
nk <- length(kids <- levels(sce$cluster_id))
ns <- length(sids <- levels(sce$sample_id))
names(kids) <- kids
names(sids) <- sids
In [75]:
# Data overview
# nb. of cells per cluster-sample
t(table(sce$cluster_id, sce$sample_id))

        
         Meristem Atrichoblast Trichoblast Exodermis Sclerenchyma Cortex
  sc_297     5242          415         298       796          380     71
  sc_298     3298          209         348       905          408    100
  sc_301     1929         1079         676       787          375    423
  sc_302     1219         1139         829      1264          561    353
        
         Endodermis Pericycle Phloem Xylem Mature root cells
  sc_297        157      1032     84   660                38
  sc_298        224      1043     58   416                37
  sc_301        147      1745    670  1069               693
  sc_302         91      1571    542   867               361
In [76]:
# Aggregation of single-cell to pseudo-bulk data
pb <- aggregateData(sce,
assay = "counts", fun = "sum",
by = c("cluster_id", "sample_id"))
In [77]:
# one sheet per sub-population
assayNames(pb)
  1. 'Meristem'
  2. 'Atrichoblast'
  3. 'Trichoblast'
  4. 'Exodermis'
  5. 'Sclerenchyma'
  6. 'Cortex'
  7. 'Endodermis'
  8. 'Pericycle'
  9. 'Phloem'
  10. 'Xylem'
  11. 'Mature root cells'
In [78]:
# pseudo-bulks for 1st sub-population
t(head(assay(pb)))
A matrix: 4 × 6 of type dbl
LOC-Os01g01010LOC-Os01g01019LOC-Os01g01030LOC-Os01g01040LOC-Os01g01050LOC-Os01g01060
sc_297367101686911831630
sc_298286 61414841181484
sc_301 3 1 2 8 2 32
sc_302 3 0 1 12 2 37
In [79]:
# Pseudo-bulk-level MDS plot
(pb_mds <- pbMDS(pb))

Removing 9400 rows with all zero counts
In [80]:
# Sample-level analysis: Pseudo-bulk methods
# construct design & contrast matrix
ei <- metadata(sce)$experiment_info
ei
mm <- model.matrix(~ 0 + ei$group_id)
mm
dimnames(mm) <- list(ei$sample_id, c(levels(ei$group_id)))
mm
contrast <- makeContrasts("gel-soil", levels = mm)
contrast
A data.frame: 4 × 3
sample_idgroup_idn_cells
<fct><fct><dbl>
sc_297gel 9173
sc_298gel 7046
sc_301soil9593
sc_302soil8797
A matrix: 4 × 2 of type dbl
ei$group_idgelei$group_idsoil
110
210
301
401
A matrix: 4 × 2 of type dbl
gelsoil
sc_29710
sc_29810
sc_30101
sc_30201
A matrix: 2 × 1 of type dbl
gel-soil
gel 1
soil-1
In [81]:
# run DS analysis
res <- pbDS(pb, design = mm, contrast = contrast,filter = "none")

  |======================================================================| 100%
In [82]:
# access results table for 1st comparison
tbl <- res$table[[1]]
In [83]:
# one data.frame per cluster
names(tbl)
  1. 'Meristem'
  2. 'Atrichoblast'
  3. 'Trichoblast'
  4. 'Exodermis'
  5. 'Sclerenchyma'
  6. 'Cortex'
  7. 'Endodermis'
  8. 'Pericycle'
  9. 'Phloem'
  10. 'Xylem'
  11. 'Mature root cells'
In [84]:
# filter FDR < 5%, abs(logFC) > log2(1.5) & sort by adj. p-value # keep 1.5 or not
tbl_fil <- lapply(tbl, function(u) {
u <- dplyr::filter(u, p_adj.loc < 0.05, abs(logFC) > log2(1.5), logCPM >=1)
dplyr::arrange(u, p_adj.loc)
})
In [85]:
# nb. of DS genes & % of total by cluster
n_de <- vapply(tbl_fil, nrow, numeric(1))
p_de <- format(n_de / nrow(sce) * 100, digits = 3)
data.frame("#DS" = n_de, "%DS" = p_de, check.names = FALSE)
A data.frame: 11 × 2
#DS%DS
<dbl><chr>
Meristem25256.128
Atrichoblast15783.830
Trichoblast14403.495
Exodermis17024.131
Sclerenchyma 7201.747
Cortex 4401.068
Endodermis 2370.575
Pericycle28486.912
Phloem 4341.053
Xylem12202.961
Mature root cells 5301.286
In [86]:
# Merge 9 data frames for each single cell type into one big data frame for the future analysis
tb2 <- resDS(sce, res, bind = "row", cpm=FALSE, frq=TRUE)
head(tb2, n = 7)
A data.frame: 7 × 15
genecluster_idsc_297.frqsc_298.frqsc_301.frqsc_302.frqgel.frqsoil.frqlogFClogCPMFp_valp_adj.locp_adj.glbcontrast
<chr><chr><dbl><dbl><dbl><dbl><dbl><dbl><dbl><dbl><dbl><dbl><dbl><dbl><chr>
1LOC-Os01g01010Meristem0.059900.067000.0015600.002460.062600.001910 1.3300 3.445.8900.015200.11400.158gel-soil
2LOC-Os01g01019Meristem0.001910.001820.0005180.000000.001870.000318-1.4100-1.260.5220.470000.86600.849gel-soil
3LOC-Os01g01030Meristem0.030000.037300.0010400.000820.032800.000953 1.2500 2.402.6900.101000.38300.454gel-soil
4LOC-Os01g01040Meristem0.116000.124000.0041500.009840.119000.006350 0.4320 4.291.6100.204000.57500.628gel-soil
5LOC-Os01g01050Meristem0.031900.031800.0010400.001640.031900.001270 0.7880 2.371.2600.261000.65500.694gel-soil
6LOC-Os01g01060Meristem0.223000.283000.0161000.026300.246000.020000 0.0679 5.740.1220.727000.93000.915gel-soil
7LOC-Os01g01070Meristem0.070600.087000.0005180.004100.076900.001910 1.5200 3.628.1000.004440.04720.070gel-soil
In [87]:
# Save all the gene expression information by Muscat
write.csv(tb2, file = "./1-DE_analysis/snRNAseq-CMPvsGel_DE_gene_list_full.csv", row.names = TRUE)
In [88]:
# filter FDR < 5%, abs(logFC) > log2(1.5) & sort by adj. p-value # keep 1.5 or not
tb2_sig <- filter(tb2, p_adj.loc<=0.05 & abs(logFC) > log2(1.5))
head (tb2_sig)
length(unique(tb2_sig$gene))
A data.frame: 6 × 15
genecluster_idsc_297.frqsc_298.frqsc_301.frqsc_302.frqgel.frqsoil.frqlogFClogCPMFp_valp_adj.locp_adj.glbcontrast
<chr><chr><dbl><dbl><dbl><dbl><dbl><dbl><dbl><dbl><dbl><dbl><dbl><dbl><chr>
1LOC-Os01g01070Meristem0.070600.087000.0005180.004100.076900.00191 1.520 3.620 8.104.44e-034.72e-027.00e-02gel-soil
2LOC-Os01g01150Meristem0.137000.174000.0036300.004920.151000.00413 1.470 4.63016.106.13e-051.49e-032.51e-03gel-soil
3LOC-Os01g01450Meristem0.114000.125000.0041500.002460.118000.00349 1.320 4.27010.601.13e-031.65e-022.58e-02gel-soil
4LOC-Os01g01510Meristem0.156000.202000.0082900.005740.174000.00731 0.849 4.920 8.363.83e-034.22e-026.31e-02gel-soil
5LOC-Os01g01570Meristem0.151000.223000.0036300.009840.179000.00604 1.240 4.94015.707.58e-051.79e-033.00e-03gel-soil
6LOC-Os01g01870Meristem0.002290.004240.0036300.005740.003040.00445-4.460-0.21547.904.47e-124.54e-109.37e-10gel-soil
5543
In [89]:
# filter out lowly detected gene
tb2_fil <- filter(tb2_sig, gel.frq >=0.1 | soil.frq >=0.1)
head (tb2_fil)
length(unique(tb2_fil$gene))
A data.frame: 6 × 15
genecluster_idsc_297.frqsc_298.frqsc_301.frqsc_302.frqgel.frqsoil.frqlogFClogCPMFp_valp_adj.locp_adj.glbcontrast
<chr><chr><dbl><dbl><dbl><dbl><dbl><dbl><dbl><dbl><dbl><dbl><dbl><dbl><chr>
1LOC-Os01g01150Meristem0.13700.1740.003630.004920.1510.004131.4704.6316.106.13e-050.001490.00251gel-soil
2LOC-Os01g01450Meristem0.11400.1250.004150.002460.1180.003491.3204.2710.601.13e-030.016500.02580gel-soil
3LOC-Os01g01510Meristem0.15600.2020.008290.005740.1740.007310.8494.92 8.363.83e-030.042200.06310gel-soil
4LOC-Os01g01570Meristem0.15100.2230.003630.009840.1790.006041.2404.9415.707.58e-050.001790.00300gel-soil
5LOC-Os01g02890Meristem0.09520.1200.002590.002460.1050.002541.5904.0812.005.36e-040.009100.01440gel-soil
6LOC-Os01g06010Meristem0.11400.1350.004670.003280.1220.004131.0304.44 8.164.28e-030.045900.06830gel-soil
2484
In [90]:
# label up vs down
tb2_fil <- tb2_fil %>% mutate(up_dn_label = case_when(logFC >=log2(1.5) ~ "Down",  
                                                      logFC <=log2(1/1.5) ~ "Up",
                                                      TRUE ~ "Not DE"))

tb2_fil$clust_up_dn <- paste(tb2_fil$cluster_id, tb2_fil$up_dn_label, sep="_")

head(tb2_fil)
A data.frame: 6 × 17
genecluster_idsc_297.frqsc_298.frqsc_301.frqsc_302.frqgel.frqsoil.frqlogFClogCPMFp_valp_adj.locp_adj.glbcontrastup_dn_labelclust_up_dn
<chr><chr><dbl><dbl><dbl><dbl><dbl><dbl><dbl><dbl><dbl><dbl><dbl><dbl><chr><chr><chr>
1LOC-Os01g01150Meristem0.13700.1740.003630.004920.1510.004131.4704.6316.106.13e-050.001490.00251gel-soilDownMeristem_Down
2LOC-Os01g01450Meristem0.11400.1250.004150.002460.1180.003491.3204.2710.601.13e-030.016500.02580gel-soilDownMeristem_Down
3LOC-Os01g01510Meristem0.15600.2020.008290.005740.1740.007310.8494.92 8.363.83e-030.042200.06310gel-soilDownMeristem_Down
4LOC-Os01g01570Meristem0.15100.2230.003630.009840.1790.006041.2404.9415.707.58e-050.001790.00300gel-soilDownMeristem_Down
5LOC-Os01g02890Meristem0.09520.1200.002590.002460.1050.002541.5904.0812.005.36e-040.009100.01440gel-soilDownMeristem_Down
6LOC-Os01g06010Meristem0.11400.1350.004670.003280.1220.004131.0304.44 8.164.28e-030.045900.06830gel-soilDownMeristem_Down
In [91]:
# Save all the filtered DE genes
write.csv(tb2_fil, file = "./1-DE_analysis/snRNAseq-CMPvsGel_DE_gene_list_q0.05_FC1.5_10percent.csv", row.names = TRUE)
In [92]:
# Number of DEGs per cell type clusters
nb_genes_per_clust <- tb2_fil %>% group_by(cluster_id) %>% tally()

nb_de_gene_count <- tb2_fil %>% group_by(gene) %>% tally(name = "n_clusters_de")

nb_cluster_DE_sig <- left_join(tb2_fil, nb_de_gene_count)

# color up and down
nb_up_dn <- tb2_fil  %>% group_by(cluster_id, up_dn_label) %>% tally(name = "n_up_dn") %>% left_join(nb_genes_per_clust)

Joining with `by = join_by(gene)`
Joining with `by = join_by(cluster_id)`
In [93]:
# Plot the number of DEGs per cell type clusters
options(repr.plot.width=16, repr.plot.height=16)

nb_v <- ggplot(data=nb_up_dn, aes(x=reorder(cluster_id, n), y=n_up_dn, fill=factor(up_dn_label, levels=c("Up", "Down")))) +
               geom_bar(stat="identity", position="stack") + ylab("Number of DEGs") + xlab("") + 
               scale_y_continuous(limits = c(0, 1500)) +
               geom_text(aes(label=n, y = n), hjust=-0.1, vjust=0.5, size=4)  + 
               theme_cowplot() + theme(plot.margin = margin(1,1,1,1, "cm"), 
               legend.title=element_blank(), 
               legend.position = c(0.7, 0.5))

(de_up_dn_bar_v <- nb_v + coord_flip())

Make the DEG number featureplot¶

In [94]:
# Copy tb2_fil for backup
tb3_fil <- tb2_fil
In [95]:
# numbers of Soil induced genes to add as metadata

(Soil_total_n <- tb3_fil %>% select(cluster_id, gene) %>% group_by(cluster_id) %>% tally(name = "total_DE"))
A tibble: 11 × 2
cluster_idtotal_DE
<chr><int>
Atrichoblast 660
Cortex 392
Endodermis 225
Exodermis 922
Mature root cells 481
Meristem 974
Pericycle 1117
Phloem 364
Sclerenchyma 517
Trichoblast 893
Xylem 645
In [96]:
# numbers of compaction up-regulated genes to add as metadata
(Soil_up_n <- tb3_fil %>% filter(up_dn_label=="Up") %>% 
 select(cluster_id, gene) %>% group_by(cluster_id) %>% tally(name = "Soil_Up"))
A tibble: 11 × 2
cluster_idSoil_Up
<chr><int>
Atrichoblast 123
Cortex 38
Endodermis 14
Exodermis 123
Mature root cells 53
Meristem 261
Pericycle 225
Phloem 49
Sclerenchyma 53
Trichoblast 80
Xylem 148
In [97]:
# numbers of compaction down-regulated genes to add as metadata
(Soil_dn_n <- tb3_fil %>% filter(up_dn_label=="Down") %>% 
 select(cluster_id, gene) %>% group_by(cluster_id) %>% tally(name = "Soil_Down"))
A tibble: 11 × 2
cluster_idSoil_Down
<chr><int>
Atrichoblast 537
Cortex 354
Endodermis 211
Exodermis 799
Mature root cells428
Meristem 713
Pericycle 892
Phloem 315
Sclerenchyma 464
Trichoblast 813
Xylem 497
In [98]:
## all genes background 
# DEG results with gene freqs
(res_to_write_frq <- resDS(sce, res, bind = "row", cpm=TRUE, frq=T))
# Output for all background genes with frequency filtering
all_bg <- filter(res_to_write_frq,
                gel.frq >=0.1 | soil.frq >=0.1)
A data.frame: 248671 × 19
genecluster_idsc_297.cpmsc_298.cpmsc_301.cpmsc_302.cpmsc_297.frqsc_298.frqsc_301.frqsc_302.frqgel.frqsoil.frqlogFClogCPMFp_valp_adj.locp_adj.glbcontrast
<chr><chr><dbl><dbl><dbl><dbl><dbl><dbl><dbl><dbl><dbl><dbl><dbl><dbl><dbl><dbl><dbl><dbl><chr>
LOC-Os01g01010Meristem11.300011.1000 4.2 4.720.0599000.0670000.0015600.002460.0626000.001910 1.3300 3.440 5.890001.52e-020.114000.15800gel-soil
LOC-Os01g01019Meristem 0.3070 0.2320 1.4 0.000.0019100.0018200.0005180.000000.0018700.000318-1.4100-1.260 0.522004.70e-010.866000.84900gel-soil
LOC-Os01g01030Meristem 5.1500 5.4600 2.8 1.570.0300000.0373000.0010400.000820.0328000.000953 1.2500 2.400 2.690001.01e-010.383000.45400gel-soil
LOC-Os01g01040Meristem21.200018.700011.218.900.1160000.1240000.0041500.009840.1190000.006350 0.4320 4.290 1.610002.04e-010.575000.62800gel-soil
LOC-Os01g01050Meristem 5.6100 4.5700 2.8 3.150.0319000.0318000.0010400.001640.0319000.001270 0.7880 2.370 1.260002.61e-010.655000.69400gel-soil
LOC-Os01g01060Meristem50.000057.400044.858.200.2230000.2830000.0161000.026300.2460000.020000 0.0679 5.740 0.122007.27e-010.930000.91500gel-soil
LOC-Os01g01070Meristem12.600012.9000 1.4 7.870.0706000.0870000.0005180.004100.0769000.001910 1.5200 3.620 8.100004.44e-030.047200.07000gel-soil
LOC-Os01g01080Meristem10.0000 9.0200 7.0 4.720.0568000.0640000.0025900.002460.0596000.002540 0.6850 3.240 1.770001.83e-010.542000.59200gel-soil
LOC-Os01g01110Meristem 0.0307 0.0000 0.0 0.000.0001910.0000000.0000000.000000.0001170.000000 1.6000-2.730 0.016408.98e-010.930000.94000gel-soil
LOC-Os01g01115Meristem 0.7670 0.6580 0.0 0.000.0045800.0048500.0000000.000000.0046800.000000 6.4400-0.265 1.820001.77e-010.532000.58900gel-soil
LOC-Os01g01120Meristem 1.1000 1.5900 0.0 0.000.0063000.0112000.0000000.000000.0082000.000000 7.3200 0.505 3.510006.09e-020.284000.35100gel-soil
LOC-Os01g01150Meristem26.200027.1000 9.8 9.440.1370000.1740000.0036300.004920.1510000.004130 1.4700 4.63016.100006.13e-050.001490.00251gel-soil
LOC-Os01g01160Meristem 1.0700 0.9290 0.0 0.000.0064900.0072800.0000000.000000.0067900.000000 6.9200 0.155 2.640001.04e-010.389000.45900gel-soil
LOC-Os01g01170Meristem 3.5600 3.6800 0.0 1.570.0195000.0252000.0000000.000820.0217000.000318 2.2700 1.860 4.150004.16e-020.223000.28500gel-soil
LOC-Os01g01250Meristem 0.0307 0.1550 0.0 0.000.0001910.0012100.0000000.000000.0005850.000000 3.5100-2.200 0.112007.38e-010.930000.91500gel-soil
LOC-Os01g01280Meristem 0.3990 0.4260 0.0 1.570.0024800.0033400.0000000.000820.0028100.000318-0.8390-0.855 0.235006.28e-010.930000.91500gel-soil
LOC-Os01g01295Meristem 6.7200 7.8200 4.2 4.720.0374000.0540000.0015600.002460.0438000.001910 0.7010 2.850 1.430002.32e-010.616000.65700gel-soil
LOC-Os01g01302Meristem 2.8800 3.0200 0.0 1.570.0151000.0215000.0000000.000820.0176000.000318 1.9800 1.580 2.940008.63e-020.353000.42000gel-soil
LOC-Os01g01307Meristem25.100027.300026.625.200.1290000.1610000.0098500.012300.1420000.010800 0.0111 4.710 0.001689.67e-010.978000.98000gel-soil
LOC-Os01g01312Meristem 6.0100 5.6500 7.0 3.150.0336000.0385000.0025900.001640.0355000.002220 0.1720 2.570 0.088507.66e-010.930000.91500gel-soil
LOC-Os01g01360Meristem 0.1840 0.0774 0.0 0.000.0009540.0006060.0000000.000000.0008200.000000 4.1000-1.900 0.203006.52e-010.930000.91500gel-soil
LOC-Os01g01380Meristem 1.9600 2.6300 0.0 0.000.0113000.0194000.0000000.000000.0144000.000000 8.0900 1.220 5.860001.55e-020.116000.15900gel-soil
LOC-Os01g01390Meristem 6.1600 6.4200 5.6 4.720.0359000.0461000.0020700.001640.0398000.001910 0.2770 2.670 0.235006.28e-010.930000.91500gel-soil
LOC-Os01g01400Meristem 1.6300 2.0500 2.8 0.000.0093500.0149000.0010400.000000.0115000.000635 0.2980 0.959 0.087807.67e-010.930000.91500gel-soil
LOC-Os01g01420Meristem 3.3400 3.7500 2.8 3.150.0196000.0261000.0010400.001640.0221000.001270 0.2530 1.870 0.117007.32e-010.930000.91500gel-soil
LOC-Os01g01430Meristem 0.0307 0.0387 0.0 0.000.0001910.0003030.0000000.000000.0002340.000000 2.3500-2.580 0.035908.50e-010.930000.91500gel-soil
LOC-Os01g01450Meristem21.400019.300011.2 4.720.1140000.1250000.0041500.002460.1180000.003490 1.3200 4.27010.600001.13e-030.016500.02580gel-soil
LOC-Os01g01510Meristem30.900033.200023.811.000.1560000.2020000.0082900.005740.1740000.007310 0.8490 4.920 8.360003.83e-030.042200.06310gel-soil
LOC-Os01g01570Meristem30.400036.2000 9.818.900.1510000.2230000.0036300.009840.1790000.006040 1.2400 4.94015.700007.58e-050.001790.00300gel-soil
LOC-Os01g01580Meristem 1.2300 1.2800 0.0 0.000.0074400.0091000.0000000.000000.0080800.000000 7.2300 0.430 3.300006.91e-020.308000.37500gel-soil
⋮⋮⋮⋮⋮⋮⋮⋮⋮⋮⋮⋮⋮⋮⋮⋮⋮⋮⋮
LOC-Os07g27290Mature root cells00.00 4.02 0.0000.0000.001440.000000.00000.000949-2.742.91 0.5170.4720000.81600.84900gel-soil
LOC-Os07g44110Mature root cells00.00 4.02 0.0000.0000.001440.000000.00000.000949-2.742.91 0.5170.4720000.81600.84900gel-soil
LOC-Os07g06920Mature root cells02.24 0.00 0.0000.0270.000000.000000.01330.000000 2.022.89 0.2050.6510000.81600.91500gel-soil
LOC-Os07g14514Mature root cells00.00 4.02 0.0000.0000.001440.000000.00000.000949-2.742.91 0.5170.4720000.81600.84900gel-soil
LOC-Os07g25330Mature root cells02.24 0.00 0.0000.0270.000000.000000.01330.000000 2.022.89 0.2050.6510000.81600.91500gel-soil
LOC-Os07g29900Mature root cells00.00 0.00 5.7900.0000.000000.002770.00000.000949-2.772.91 0.5320.4660000.81600.84900gel-soil
LOC-Os08g18810Mature root cells02.24 0.00 0.0000.0270.000000.000000.01330.000000 2.022.89 0.2050.6510000.81600.91500gel-soil
LOC-Os08g35820Mature root cells02.24 0.00 0.0000.0270.000000.000000.01330.000000 2.022.89 0.2050.6510000.81600.91500gel-soil
LOC-Os08g36920Mature root cells00.0024.1017.4000.0000.005770.008310.00000.006640-5.713.8813.2000.0002820.01310.00868gel-soil
LOC-Os08g07140Mature root cells02.24 0.00 0.0000.0270.000000.000000.01330.000000 2.022.89 0.2050.6510000.81600.91500gel-soil
LOC-Os08g25860Mature root cells02.24 0.00 0.0000.0270.000000.000000.01330.000000 2.022.89 0.2050.6510000.81600.91500gel-soil
LOC-Os10g26010Mature root cells00.00 4.02 0.0000.0000.001440.000000.00000.000949-2.742.91 0.5170.4720000.81600.84900gel-soil
LOC-Os11g02880Mature root cells00.00 4.02 0.0000.0000.001440.000000.00000.000949-2.742.91 0.5170.4720000.81600.84900gel-soil
LOC-Os03g05930Mature root cells00.00 0.00 5.7900.0000.000000.002770.00000.000949-2.772.91 0.5320.4660000.81600.84900gel-soil
LOC-Os06g11550Mature root cells00.00 0.00 5.7900.0000.000000.002770.00000.000949-2.772.91 0.5320.4660000.81600.84900gel-soil
LOC-Os06g20750Mature root cells00.00 4.02 0.0000.0000.001440.000000.00000.000949-2.742.91 0.5170.4720000.81600.84900gel-soil
LOC-Os10g32100Mature root cells00.00 4.02 0.0000.0000.001440.000000.00000.000949-2.742.91 0.5170.4720000.81600.84900gel-soil
LOC-Os02g16830Mature root cells00.00 4.02 0.0000.0000.001440.000000.00000.000949-2.742.91 0.5170.4720000.81600.84900gel-soil
LOC-Os03g36239Mature root cells00.00 0.00 5.7900.0000.000000.002770.00000.000949-2.772.91 0.5320.4660000.81600.84900gel-soil
LOC-Os01g50670Mature root cells00.00 0.00 5.7900.0000.000000.002770.00000.000949-2.772.91 0.5320.4660000.81600.84900gel-soil
LOC-Os10g05740Mature root cells00.00 4.02 0.0000.0000.001440.000000.00000.000949-2.742.91 0.5170.4720000.81600.84900gel-soil
LOC-Os10g37560Mature root cells00.00 4.02 0.0000.0000.001440.000000.00000.000949-2.742.91 0.5170.4720000.81600.84900gel-soil
LOC-Os04g49810Mature root cells00.00 4.02 0.0000.0000.001440.000000.00000.000949-2.742.91 0.5170.4720000.81600.84900gel-soil
LOC-Os05g24520Mature root cells00.00 4.02 0.0000.0000.001440.000000.00000.000949-2.742.91 0.5170.4720000.81600.84900gel-soil
LOC-Os05g49090Mature root cells00.00 4.02 0.0000.0000.001440.000000.00000.000949-2.742.91 0.5170.4720000.81600.84900gel-soil
LOC-Os09g03830Mature root cells00.00 4.02 0.0000.0000.001440.000000.00000.000949-2.742.91 0.5170.4720000.81600.84900gel-soil
LOC-Os03g25010Mature root cells00.00 0.00 5.7900.0000.000000.002770.00000.000949-2.772.91 0.5320.4660000.81600.84900gel-soil
LOC-Os04g06400Mature root cells00.00 0.00 5.7900.0000.000000.002770.00000.000949-2.772.91 0.5320.4660000.81600.84900gel-soil
LOC-Os06g21440Mature root cells00.00 0.00 5.7900.0000.000000.002770.00000.000949-2.772.91 0.5320.4660000.81600.84900gel-soil
LOC-Os09g39170Mature root cells00.00 0.0017.4000.0000.000000.008310.00000.002850-4.233.22 3.4200.0644000.50800.36200gel-soil
In [99]:
# Get the total gene detected for each cluster
(bg_n <- all_bg %>% 
 select(cluster_id, gene) %>% 
group_by(cluster_id) %>% 
tally(name = "All_genes"))
A tibble: 11 × 2
cluster_idAll_genes
<chr><int>
Atrichoblast 1654
Cortex 1853
Endodermis 2777
Exodermis 2181
Mature root cells3804
Meristem 2180
Pericycle 2120
Phloem 2313
Sclerenchyma 1877
Trichoblast 2298
Xylem 2056
In [100]:
# Make a metadata for UMAP presentation
(de_meta_for_umap <- data.frame("barcode"=colnames(rc.comparison), 
                               "cluster_id"=rc.comparison$manual.anno))
A data.frame: 34609 × 2
barcodecluster_id
<chr><fct>
AAACCCAAGATGAATC_1AAACCCAAGATGAATC_1Exodermis
AAACCCAAGGACGCTA_1AAACCCAAGGACGCTA_1Pericycle
AAACCCAAGGATATGT_1AAACCCAAGGATATGT_1Atrichoblast
AAACCCAAGGCACCAA_1AAACCCAAGGCACCAA_1Cortex
AAACCCAAGTCCCTAA_1AAACCCAAGTCCCTAA_1Exodermis
AAACCCACAACCCGCA_1AAACCCACAACCCGCA_1Meristem
AAACCCACAACTCCCT_1AAACCCACAACTCCCT_1Exodermis
AAACCCACAATTGCTG_1AAACCCACAATTGCTG_1Sclerenchyma
AAACCCACACATATCG_1AAACCCACACATATCG_1Atrichoblast
AAACCCACAGACAAAT_1AAACCCACAGACAAAT_1Meristem
AAACCCACAGCAAGAC_1AAACCCACAGCAAGAC_1Meristem
AAACCCACAGTAGATA_1AAACCCACAGTAGATA_1Meristem
AAACCCACATCGTGGC_1AAACCCACATCGTGGC_1Meristem
AAACCCAGTGAGATAT_1AAACCCAGTGAGATAT_1Meristem
AAACCCAGTGTAACGG_1AAACCCAGTGTAACGG_1Sclerenchyma
AAACCCAGTTCCAGGC_1AAACCCAGTTCCAGGC_1Pericycle
AAACCCATCTGAGAAA_1AAACCCATCTGAGAAA_1Pericycle
AAACGAAAGAGTCAGC_1AAACGAAAGAGTCAGC_1Trichoblast
AAACGAAAGAGTCCGA_1AAACGAAAGAGTCCGA_1Trichoblast
AAACGAAAGCTAGATA_1AAACGAAAGCTAGATA_1Meristem
AAACGAAAGGAACGCT_1AAACGAAAGGAACGCT_1Meristem
AAACGAACACGAGAAC_1AAACGAACACGAGAAC_1Meristem
AAACGAAGTGGTTTAC_1AAACGAAGTGGTTTAC_1Meristem
AAACGAATCACGGAGA_1AAACGAATCACGGAGA_1Pericycle
AAACGAATCATGAGTC_1AAACGAATCATGAGTC_1Meristem
AAACGAATCCCAGTGG_1AAACGAATCCCAGTGG_1Meristem
AAACGCTCAAAGCACG_1AAACGCTCAAAGCACG_1Meristem
AAACGCTCAACTAGAA_1AAACGCTCAACTAGAA_1Meristem
AAACGCTCACAGTCAT_1AAACGCTCACAGTCAT_1Exodermis
AAACGCTCACATTCGA_1AAACGCTCACATTCGA_1Meristem
⋮⋮⋮
TTTGACTGTATGTCTG_8TTTGACTGTATGTCTG_8Xylem
TTTGACTGTCCAAATC_8TTTGACTGTCCAAATC_8Pericycle
TTTGACTGTGTCTCCT_8TTTGACTGTGTCTCCT_8Exodermis
TTTGACTTCAGACATC_8TTTGACTTCAGACATC_8Pericycle
TTTGACTTCCATCTAT_8TTTGACTTCCATCTAT_8Sclerenchyma
TTTGACTTCCCGAGAC_8TTTGACTTCCCGAGAC_8Atrichoblast
TTTGACTTCCGATTAG_8TTTGACTTCCGATTAG_8Exodermis
TTTGGAGCACTATCCC_8TTTGGAGCACTATCCC_8Pericycle
TTTGGTTAGCCACCGT_8TTTGGTTAGCCACCGT_8Sclerenchyma
TTTGGTTAGGCCTTGC_8TTTGGTTAGGCCTTGC_8Pericycle
TTTGGTTAGTAACCGG_8TTTGGTTAGTAACCGG_8Atrichoblast
TTTGGTTCAACACACT_8TTTGGTTCAACACACT_8Exodermis
TTTGGTTCACACACTA_8TTTGGTTCACACACTA_8Meristem
TTTGGTTCACATTGTG_8TTTGGTTCACATTGTG_8Meristem
TTTGGTTCACTTCCTG_8TTTGGTTCACTTCCTG_8Trichoblast
TTTGGTTCAGCTATAC_8TTTGGTTCAGCTATAC_8Xylem
TTTGGTTCATGACTTG_8TTTGGTTCATGACTTG_8Sclerenchyma
TTTGGTTGTAACCCTA_8TTTGGTTGTAACCCTA_8Phloem
TTTGGTTGTATGAGCG_8TTTGGTTGTATGAGCG_8Phloem
TTTGGTTGTCTAACGT_8TTTGGTTGTCTAACGT_8Exodermis
TTTGGTTTCACTAGCA_8TTTGGTTTCACTAGCA_8Sclerenchyma
TTTGGTTTCAGTCTTT_8TTTGGTTTCAGTCTTT_8Pericycle
TTTGGTTTCATTTGTC_8TTTGGTTTCATTTGTC_8Xylem
TTTGTTGGTCAACCAT_8TTTGTTGGTCAACCAT_8Pericycle
TTTGTTGTCATTACTC_8TTTGTTGTCATTACTC_8Endodermis
TTTGTTGTCCGCTGTT_8TTTGTTGTCCGCTGTT_8Trichoblast
TTTGTTGTCCTACCGT_8TTTGTTGTCCTACCGT_8Sclerenchyma
TTTGTTGTCGGTCATA_8TTTGTTGTCGGTCATA_8Mature root cells
TTTGTTGTCTCGGTCT_8TTTGTTGTCTCGGTCT_8Phloem
TTTGTTGTCTGATTCT_8TTTGTTGTCTGATTCT_8Phloem
In [101]:
# Add the quantified DEG number into the metadata
de_meta_for_umap <- left_join(de_meta_for_umap, bg_n)

de_meta_for_umap <- left_join(de_meta_for_umap, Soil_total_n)

de_meta_for_umap <- left_join(de_meta_for_umap, Soil_up_n)

de_meta_for_umap <- left_join(de_meta_for_umap, Soil_dn_n)
head(de_meta_for_umap, n =7)

Joining with `by = join_by(cluster_id)`
Joining with `by = join_by(cluster_id)`
Joining with `by = join_by(cluster_id)`
Joining with `by = join_by(cluster_id)`
A data.frame: 7 × 6
barcodecluster_idAll_genestotal_DESoil_UpSoil_Down
<chr><chr><int><int><int><int>
1AAACCCAAGATGAATC_1Exodermis 2181 922123799
2AAACCCAAGGACGCTA_1Pericycle 21201117225892
3AAACCCAAGGATATGT_1Atrichoblast1654 660123537
4AAACCCAAGGCACCAA_1Cortex 1853 392 38354
5AAACCCAAGTCCCTAA_1Exodermis 2181 922123799
6AAACCCACAACCCGCA_1Meristem 2180 974261713
7AAACCCACAACTCCCT_1Exodermis 2181 922123799
In [102]:
# replace NA with zero for catagories that were too small to test 

de_meta_for_umap[is.na(de_meta_for_umap)] <- 0
In [103]:
# Calculate the percentage for DEG number
de_meta_for_umap <- mutate(de_meta_for_umap, 
                          Percent_DE=(total_DE/All_genes)*100,
                          Percent_Up=(Soil_Up/All_genes)*100,
                          Percent_Dn=(Soil_Down/All_genes)*100)
head(de_meta_for_umap, n =10)
A data.frame: 10 × 9
barcodecluster_idAll_genestotal_DESoil_UpSoil_DownPercent_DEPercent_UpPercent_Dn
<chr><chr><int><int><int><int><dbl><dbl><dbl>
1AAACCCAAGATGAATC_1Exodermis 2181 92212379942.27419 5.63961536.63457
2AAACCCAAGGACGCTA_1Pericycle 2120111722589252.6886810.61320842.07547
3AAACCCAAGGATATGT_1Atrichoblast1654 66012353739.90326 7.43651832.46675
4AAACCCAAGGCACCAA_1Cortex 1853 392 3835421.15488 2.05072919.10416
5AAACCCAAGTCCCTAA_1Exodermis 2181 92212379942.27419 5.63961536.63457
6AAACCCACAACCCGCA_1Meristem 2180 97426171344.6789011.97247732.70642
7AAACCCACAACTCCCT_1Exodermis 2181 92212379942.27419 5.63961536.63457
8AAACCCACAATTGCTG_1Sclerenchyma1877 517 5346427.54395 2.82365524.72030
9AAACCCACACATATCG_1Atrichoblast1654 66012353739.90326 7.43651832.46675
10AAACCCACAGACAAAT_1Meristem 2180 97426171344.6789011.97247732.70642
In [104]:
total_de_meta <- de_meta_for_umap$total_DE
names(total_de_meta) <- colnames(rc.comparison)

rc.comparison <- AddMetaData(
  object = rc.comparison,
  metadata = total_de_meta,
  col.name = 'total_DE')

up_de_meta <- de_meta_for_umap$Soil_Up
names(up_de_meta) <- colnames(rc.comparison)

rc.comparison <- AddMetaData(
  object = rc.comparison,
  metadata = up_de_meta,
  col.name = 'Soil_Up')


dn_de_meta <- de_meta_for_umap$Soil_Down
names(dn_de_meta) <- colnames(rc.comparison)

rc.comparison <- AddMetaData(
  object = rc.comparison,
  metadata = dn_de_meta,
  col.name = 'Soil_Down')
In [105]:
options(repr.plot.width=16, repr.plot.height=16)
FeaturePlot(rc.comparison, 
            features = c("total_DE"), 
            max.cutoff = 1000, 
            min.cutoff = 600,
                         label=F, 
                         order = T, 
                         cols=c("beige", "#01665e"), 
                         pt.size = 0.5) + 
                            ggtitle("Total Com DE genes") +  
                            theme_void(base_size = 16) + 
                            theme(plot.title = element_text(hjust = 0.5)) +
                                 labs(color="# genes") +  theme(plot.margin = margin(0.5,0.5,0.5,0.5, "cm"))
In [ ]:
In [ ]:

Combining genes with up-regulation/down-regulation for GO term analysis¶

In [134]:
## GO term analysis for DEGs
# 
markers_sel_all <- select(tb2_fil, gene, cluster_id)

markers_list_all <- split(markers_sel_all, f=markers_sel_all$cluster_id)
 
#this makes list from long df of gene lists - TARGET is what we want to keep
markers_list_all  <- lapply(markers_list_all, function(x) x[names(x)=="gene"])
# convert each sublist into character and eliminate duplicates
markers_list_all  <- lapply(markers_list_all, function(x) as.character(unique(x$gene)))
In [135]:
# Change the format of gene ID to make it recognizable: change"-" to "_"
for (i in 1:length(markers_list_all)){
    markers_list_all[[i]] <- gsub("LOC-","LOC_",markers_list_all[[i]])
} 
head(markers_list_all, n=1)
$Atrichoblast =
  1. 'LOC_Os01g01150'
  2. 'LOC_Os01g01570'
  3. 'LOC_Os01g02890'
  4. 'LOC_Os01g09030'
  5. 'LOC_Os01g09560'
  6. 'LOC_Os01g09760'
  7. 'LOC_Os01g11054'
  8. 'LOC_Os01g11414'
  9. 'LOC_Os01g11580'
  10. 'LOC_Os01g11900'
  11. 'LOC_Os01g15830'
  12. 'LOC_Os01g25484'
  13. 'LOC_Os01g28989'
  14. 'LOC_Os01g29820'
  15. 'LOC_Os01g35789'
  16. 'LOC_Os01g35930'
  17. 'LOC_Os01g36229'
  18. 'LOC_Os01g37950'
  19. 'LOC_Os01g38229'
  20. 'LOC_Os01g40560'
  21. 'LOC_Os01g40870'
  22. 'LOC_Os01g42520'
  23. 'LOC_Os01g46070'
  24. 'LOC_Os01g46980'
  25. 'LOC_Os01g49190'
  26. 'LOC_Os01g49310'
  27. 'LOC_Os01g52500'
  28. 'LOC_Os01g52810'
  29. 'LOC_Os01g53294'
  30. 'LOC_Os01g55260'
  31. 'LOC_Os01g56590'
  32. 'LOC_Os01g56910'
  33. 'LOC_Os01g58459'
  34. 'LOC_Os01g62020'
  35. 'LOC_Os01g63710'
  36. 'LOC_Os01g64010'
  37. 'LOC_Os01g65530'
  38. 'LOC_Os01g67134'
  39. 'LOC_Os01g67220'
  40. 'LOC_Os01g67364'
  41. 'LOC_Os01g67480'
  42. 'LOC_Os01g68020'
  43. 'LOC_Os01g68324'
  44. 'LOC_Os01g69850'
  45. 'LOC_Os01g70270'
  46. 'LOC_Os01g70470'
  47. 'LOC_Os01g71630'
  48. 'LOC_Os01g74410'
  49. 'LOC_Os01g74640'
  50. 'LOC_Os01g01520'
  51. 'LOC_Os01g01960'
  52. 'LOC_Os01g02940'
  53. 'LOC_Os01g03020'
  54. 'LOC_Os01g05490'
  55. 'LOC_Os01g07500'
  56. 'LOC_Os01g07570'
  57. 'LOC_Os01g08700'
  58. 'LOC_Os01g09370'
  59. 'LOC_Os01g09860'
  60. 'LOC_Os01g10680'
  61. 'LOC_Os01g15270'
  62. 'LOC_Os01g18170'
  63. 'LOC_Os01g18744'
  64. 'LOC_Os01g22010'
  65. 'LOC_Os01g22490'
  66. 'LOC_Os01g23590'
  67. 'LOC_Os01g25920'
  68. 'LOC_Os01g26039'
  69. 'LOC_Os01g33960'
  70. 'LOC_Os01g42700'
  71. 'LOC_Os01g45880'
  72. 'LOC_Os01g47780'
  73. 'LOC_Os01g51290'
  74. 'LOC_Os01g51840'
  75. 'LOC_Os01g56140'
  76. 'LOC_Os01g56780'
  77. 'LOC_Os01g59880'
  78. 'LOC_Os01g60040'
  79. 'LOC_Os01g64490'
  80. 'LOC_Os01g66580'
  81. 'LOC_Os01g67370'
  82. 'LOC_Os01g67500'
  83. 'LOC_Os01g67860'
  84. 'LOC_Os01g68810'
  85. 'LOC_Os01g69920'
  86. 'LOC_Os01g70720'
  87. 'LOC_Os01g71114'
  88. 'LOC_Os01g73080'
  89. 'LOC_Os01g73514'
  90. 'LOC_Os10g04342'
  91. 'LOC_Os10g08599'
  92. 'LOC_Os10g09200'
  93. 'LOC_Os10g10580'
  94. 'LOC_Os10g13694'
  95. 'LOC_Os10g17280'
  96. 'LOC_Os10g25487'
  97. 'LOC_Os10g27274'
  98. 'LOC_Os10g29560'
  99. 'LOC_Os10g30080'
  100. 'LOC_Os10g31660'
  101. 'LOC_Os10g33800'
  102. 'LOC_Os10g35110'
  103. 'LOC_Os10g35770'
  104. 'LOC_Os10g39140'
  105. 'LOC_Os10g39890'
  106. 'LOC_Os10g40220'
  107. 'LOC_Os10g40730'
  108. 'LOC_Os10g40790'
  109. 'LOC_Os10g02630'
  110. 'LOC_Os10g08550'
  111. 'LOC_Os10g11870'
  112. 'LOC_Os10g15310'
  113. 'LOC_Os10g16640'
  114. 'LOC_Os10g22570'
  115. 'LOC_Os10g24094'
  116. 'LOC_Os10g25090'
  117. 'LOC_Os10g25770'
  118. 'LOC_Os10g28510'
  119. 'LOC_Os10g30951'
  120. 'LOC_Os10g30970'
  121. 'LOC_Os10g31730'
  122. 'LOC_Os10g36924'
  123. 'LOC_Os10g40510'
  124. 'LOC_Os10g40530'
  125. 'LOC_Os10g42299'
  126. 'LOC_Os11g01074'
  127. 'LOC_Os11g01140'
  128. 'LOC_Os11g01154'
  129. 'LOC_Os11g01380'
  130. 'LOC_Os11g01570'
  131. 'LOC_Os11g05562'
  132. 'LOC_Os11g06934'
  133. 'LOC_Os11g12000'
  134. 'LOC_Os11g14220'
  135. 'LOC_Os11g16530'
  136. 'LOC_Os11g17290'
  137. 'LOC_Os11g23880'
  138. 'LOC_Os11g25920'
  139. 'LOC_Os11g26594'
  140. 'LOC_Os11g26860'
  141. 'LOC_Os11g43404'
  142. 'LOC_Os11g44870'
  143. 'LOC_Os11g45130'
  144. 'LOC_Os11g45280'
  145. 'LOC_Os11g47370'
  146. 'LOC_Os11g01340'
  147. 'LOC_Os11g04409'
  148. 'LOC_Os11g05050'
  149. 'LOC_Os11g06720'
  150. 'LOC_Os11g06890'
  151. 'LOC_Os11g08210'
  152. 'LOC_Os11g14070'
  153. 'LOC_Os11g14544'
  154. 'LOC_Os11g20239'
  155. 'LOC_Os11g20310'
  156. 'LOC_Os11g20330'
  157. 'LOC_Os11g21990'
  158. 'LOC_Os11g30370'
  159. 'LOC_Os11g31890'
  160. 'LOC_Os11g34150'
  161. 'LOC_Os11g34230'
  162. 'LOC_Os11g34650'
  163. 'LOC_Os11g36470'
  164. 'LOC_Os11g39530'
  165. 'LOC_Os11g41820'
  166. 'LOC_Os11g42800'
  167. 'LOC_Os12g01140'
  168. 'LOC_Os12g02750'
  169. 'LOC_Os12g05660'
  170. 'LOC_Os12g07530'
  171. 'LOC_Os12g07670'
  172. 'LOC_Os12g09550'
  173. 'LOC_Os12g13440'
  174. 'LOC_Os12g16350'
  175. 'LOC_Os12g18729'
  176. 'LOC_Os12g20144'
  177. 'LOC_Os12g22760'
  178. 'LOC_Os12g25690'
  179. 'LOC_Os12g30540'
  180. 'LOC_Os12g32536'
  181. 'LOC_Os12g33946'
  182. 'LOC_Os12g33958'
  183. 'LOC_Os12g34094'
  184. 'LOC_Os12g37410'
  185. 'LOC_Os12g38180'
  186. 'LOC_Os12g40900'
  187. 'LOC_Os12g42884'
  188. 'LOC_Os12g43600'
  189. 'LOC_Os12g44150'
  190. 'LOC_Os12g02660'
  191. 'LOC_Os12g03080'
  192. 'LOC_Os12g06040'
  193. 'LOC_Os12g13720'
  194. 'LOC_Os12g14840'
  195. 'LOC_Os12g14930'
  196. 'LOC_Os12g15222'
  197. 'LOC_Os12g18120'
  198. 'LOC_Os12g19350'
  199. 'LOC_Os12g20390'
  200. 'LOC_Os12g23570'
  201. ⋯
  202. 'LOC_Os05g35170'
  203. 'LOC_Os05g35980'
  204. 'LOC_Os05g36120'
  205. 'LOC_Os05g39960'
  206. 'LOC_Os05g40200'
  207. 'LOC_Os05g40820'
  208. 'LOC_Os05g40900'
  209. 'LOC_Os05g43570'
  210. 'LOC_Os05g46240'
  211. 'LOC_Os05g46580'
  212. 'LOC_Os05g48620'
  213. 'LOC_Os05g50420'
  214. 'LOC_Os05g50750'
  215. 'LOC_Os05g51500'
  216. 'LOC_Os05g51560'
  217. 'LOC_Os05g51790'
  218. 'LOC_Os05g51830'
  219. 'LOC_Os06g01260'
  220. 'LOC_Os06g02550'
  221. 'LOC_Os06g04399'
  222. 'LOC_Os06g08080'
  223. 'LOC_Os06g09320'
  224. 'LOC_Os06g12170'
  225. 'LOC_Os06g14406'
  226. 'LOC_Os06g21730'
  227. 'LOC_Os06g22919'
  228. 'LOC_Os06g22960'
  229. 'LOC_Os06g23504'
  230. 'LOC_Os06g23870'
  231. 'LOC_Os06g37560'
  232. 'LOC_Os06g39600'
  233. 'LOC_Os06g39700'
  234. 'LOC_Os06g43120'
  235. 'LOC_Os06g43850'
  236. 'LOC_Os06g44034'
  237. 'LOC_Os06g44410'
  238. 'LOC_Os06g44970'
  239. 'LOC_Os06g46149'
  240. 'LOC_Os06g47820'
  241. 'LOC_Os06g48940'
  242. 'LOC_Os06g51150'
  243. 'LOC_Os06g01500'
  244. 'LOC_Os06g03710'
  245. 'LOC_Os06g04560'
  246. 'LOC_Os06g06000'
  247. 'LOC_Os06g07040'
  248. 'LOC_Os06g08740'
  249. 'LOC_Os06g11860'
  250. 'LOC_Os06g12310'
  251. 'LOC_Os06g12590'
  252. 'LOC_Os06g15779'
  253. 'LOC_Os06g16919'
  254. 'LOC_Os06g23770'
  255. 'LOC_Os06g24594'
  256. 'LOC_Os06g25500'
  257. 'LOC_Os06g28144'
  258. 'LOC_Os06g29380'
  259. 'LOC_Os06g29650'
  260. 'LOC_Os06g30901'
  261. 'LOC_Os06g30950'
  262. 'LOC_Os06g36740'
  263. 'LOC_Os06g37180'
  264. 'LOC_Os06g43210'
  265. 'LOC_Os06g43940'
  266. 'LOC_Os06g43980'
  267. 'LOC_Os06g44620'
  268. 'LOC_Os06g46890'
  269. 'LOC_Os06g48750'
  270. 'LOC_Os06g50300'
  271. 'LOC_Os06g51510'
  272. 'LOC_Os07g01904'
  273. 'LOC_Os07g04550'
  274. 'LOC_Os07g12780'
  275. 'LOC_Os07g12800'
  276. 'LOC_Os07g13460'
  277. 'LOC_Os07g14270'
  278. 'LOC_Os07g14850'
  279. 'LOC_Os07g16140'
  280. 'LOC_Os07g22390'
  281. 'LOC_Os07g28940'
  282. 'LOC_Os07g31599'
  283. 'LOC_Os07g32600'
  284. 'LOC_Os07g34580'
  285. 'LOC_Os07g35860'
  286. 'LOC_Os07g38530'
  287. 'LOC_Os07g43870'
  288. 'LOC_Os07g45320'
  289. 'LOC_Os07g47990'
  290. 'LOC_Os07g49460'
  291. 'LOC_Os07g07000'
  292. 'LOC_Os07g07990'
  293. 'LOC_Os07g09580'
  294. 'LOC_Os07g10250'
  295. 'LOC_Os07g13234'
  296. 'LOC_Os07g23270'
  297. 'LOC_Os07g23480'
  298. 'LOC_Os07g23930'
  299. 'LOC_Os07g27140'
  300. 'LOC_Os07g30970'
  301. 'LOC_Os07g31300'
  302. 'LOC_Os07g33300'
  303. 'LOC_Os07g37310'
  304. 'LOC_Os07g37750'
  305. 'LOC_Os07g40640'
  306. 'LOC_Os07g41600'
  307. 'LOC_Os07g44060'
  308. 'LOC_Os07g46690'
  309. 'LOC_Os07g48244'
  310. 'LOC_Os07g48410'
  311. 'LOC_Os07g49280'
  312. 'LOC_Os08g01930'
  313. 'LOC_Os08g02120'
  314. 'LOC_Os08g03290'
  315. 'LOC_Os08g03579'
  316. 'LOC_Os08g04270'
  317. 'LOC_Os08g07010'
  318. 'LOC_Os08g09230'
  319. 'LOC_Os08g11470'
  320. 'LOC_Os08g11480'
  321. 'LOC_Os08g14109'
  322. 'LOC_Os08g14850'
  323. 'LOC_Os08g14860'
  324. 'LOC_Os08g14880'
  325. 'LOC_Os08g16480'
  326. 'LOC_Os08g19114'
  327. 'LOC_Os08g19590'
  328. 'LOC_Os08g22354'
  329. 'LOC_Os08g29615'
  330. 'LOC_Os08g30770'
  331. 'LOC_Os08g33100'
  332. 'LOC_Os08g33479'
  333. 'LOC_Os08g33740'
  334. 'LOC_Os08g38210'
  335. 'LOC_Os08g38560'
  336. 'LOC_Os08g02400'
  337. 'LOC_Os08g04920'
  338. 'LOC_Os08g06380'
  339. 'LOC_Os08g07970'
  340. 'LOC_Os08g08586'
  341. 'LOC_Os08g08592'
  342. 'LOC_Os08g09350'
  343. 'LOC_Os08g12430'
  344. 'LOC_Os08g14460'
  345. 'LOC_Os08g17370'
  346. 'LOC_Os08g20544'
  347. 'LOC_Os08g21760'
  348. 'LOC_Os08g22864'
  349. 'LOC_Os08g23180'
  350. 'LOC_Os08g32100'
  351. 'LOC_Os08g33120'
  352. 'LOC_Os08g33370'
  353. 'LOC_Os08g33920'
  354. 'LOC_Os08g34280'
  355. 'LOC_Os08g34879'
  356. 'LOC_Os08g37320'
  357. 'LOC_Os08g37444'
  358. 'LOC_Os08g42000'
  359. 'LOC_Os08g43130'
  360. 'LOC_Os08g43400'
  361. 'LOC_Os09g00999'
  362. 'LOC_Os09g01000'
  363. 'LOC_Os09g02650'
  364. 'LOC_Os09g04290'
  365. 'LOC_Os09g04300'
  366. 'LOC_Os09g06634'
  367. 'LOC_Os09g07640'
  368. 'LOC_Os09g08910'
  369. 'LOC_Os09g09360'
  370. 'LOC_Os09g12970'
  371. 'LOC_Os09g17049'
  372. 'LOC_Os09g19734'
  373. 'LOC_Os09g20350'
  374. 'LOC_Os09g24440'
  375. 'LOC_Os09g26770'
  376. 'LOC_Os09g29930'
  377. 'LOC_Os09g31080'
  378. 'LOC_Os09g32080'
  379. 'LOC_Os09g39500'
  380. 'LOC_Os09g02700'
  381. 'LOC_Os09g04504'
  382. 'LOC_Os09g07300'
  383. 'LOC_Os09g08890'
  384. 'LOC_Os09g10054'
  385. 'LOC_Os09g14610'
  386. 'LOC_Os09g19350'
  387. 'LOC_Os09g21689'
  388. 'LOC_Os09g22505'
  389. 'LOC_Os09g25880'
  390. 'LOC_Os09g27744'
  391. 'LOC_Os09g27970'
  392. 'LOC_Os09g29404'
  393. 'LOC_Os09g30486'
  394. 'LOC_Os09g31180'
  395. 'LOC_Os09g31220'
  396. 'LOC_Os09g37006'
  397. 'LOC_Os09g38790'
  398. 'EPlORYSAT000373608'
  399. 'EPlORYSAT000373647'
  400. 'EPlORYSAT000373869'
  401. 'ChrSy.fgenesh.gene.29'
In [136]:
# Remove all the gene IDs which does not follow "LOC_OS" format
for (i in 1:length(markers_list_all)){
    markers_list_all[[i]] <- markers_list_all[[i]][grep("LOC_",markers_list_all[[i]])]
}
In [137]:
# Load the MSU-RAP ID converter table downloaded from https://rapdb.dna.affrc.go.jp/download/irgsp1.html
msu2rap <- read.table("./ID_conversion/RAP-MSU_2023-03-15.txt.gz")
In [138]:
# Convert the MSU ID to RAP ID if the MSU ID can be found in V2 column in msu2rap table
# grep does not require exact mtach
markers_list_all2 <- markers_list_all
for (i in 1:length(markers_list_all2)){
    for (j in 1:length(markers_list_all2[[i]])){
    suppressMessages(markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j],msu2rap$V2)])  
    } 
}
## There will be warning message because RAP and MSU are not strictly one to one

Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list_all2[[i]][j] <- msu2rap$V1[grep(markers_list_all2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
In [140]:
#Check whether conversion works
markers_list_all2[[1]]
  1. 'Os01g0101600'
  2. 'Os01g0105400'
  3. 'Os01g0118300'
  4. 'Os01g0185500'
  5. 'Os01g0191500'
  6. 'Os01g0193900'
  7. 'Os01g0208700'
  8. 'Os01g0212400'
  9. 'Os01g0214300'
  10. 'Os01g0218032'
  11. 'Os01g0263300'
  12. 'Os01g0357100'
  13. 'Os01g0386700'
  14. 'Os01g0392800'
  15. 'Os01g0539400'
  16. 'Os01g0541000'
  17. 'Os01g0543000'
  18. 'Os01g0559900'
  19. 'Os01g0563000'
  20. 'Os01g0588100'
  21. 'Os01g0591300'
  22. 'Os01g0611000'
  23. 'Os01g0649100'
  24. 'Os01g0659200'
  25. 'Os01g0685800'
  26. 'Os01g0687300'
  27. 'Os01g0723400'
  28. 'Os01g0728400'
  29. 'Os01g0734200'
  30. 'Os01g0757400'
  31. 'Os01g0772700'
  32. 'Os01g0777000'
  33. 'Os01g0798100'
  34. 'Os01g0837300'
  35. 'Os01g0855900'
  36. 'Os01g0859400'
  37. 'Os01g0876500'
  38. 'Os01g0896800'
  39. 'Os01g0897600'
  40. 'Os01g0899387'
  41. 'Os01g0900800'
  42. 'Os01g0908200'
  43. 'Os01g0911200'
  44. 'Os01g0922800'
  45. 'Os01g0927600'
  46. 'Os01g0930200'
  47. 'Os01g0944200'
  48. 'Os01g0975300'
  49. 'Os01g0978000'
  50. 'Os01g0104900'
  51. 'Os01g0109700'
  52. 'Os01g0119050'
  53. 'Os01g0120300'
  54. 'Os01g0147900'
  55. 'Os01g0169800'
  56. 'Os01g0170500'
  57. 'Os01g0182600'
  58. 'Os01g0188900'
  59. 'Os01g0195200'
  60. 'Os01g0203800'
  61. 'Os01g0256500'
  62. 'Os01g0284500'
  63. 'Os01g0291500'
  64. 'Os01g0323600'
  65. 'Os01g0328400'
  66. 'Os01g0337600'
  67. 'Os01g0361000'
  68. 'Os01g0362100'
  69. 'None'
  70. 'Os01g0612600'
  71. 'Os01g0646700'
  72. 'Os01g0668100'
  73. 'Os01g0709500'
  74. 'Os01g0716200'
  75. 'Os01g0767000'
  76. 'Os01g0775100'
  77. 'Os01g0814200'
  78. 'Os01g0816400'
  79. 'Os01g0864700'
  80. 'Os01g0889200'
  81. 'Os01g0899500'
  82. 'Os01g0901000'
  83. 'Os01g0905800'
  84. 'Os01g0916800'
  85. 'Os01g0923700'
  86. 'Os01g0933400'
  87. 'Os01g0937400'
  88. 'Os01g0961600'
  89. 'Os01g0966000'
  90. 'Os10g0132700'
  91. 'Os10g0167700'
  92. 'Os10g0172600'
  93. 'Os10g0185200'
  94. 'Os10g0204300'
  95. 'Os10g0320400'
  96. 'Os10g0394400'
  97. 'Os10g0412600'
  98. 'Os10g0431000'
  99. 'Os10g0437000'
  100. 'Os10g0454200'
  101. 'Os10g0478200'
  102. 'Os10g0493600'
  103. 'Os10g0501500'
  104. 'Os10g0536400'
  105. 'Os10g0546100'
  106. 'None'
  107. 'Os10g0556100'
  108. 'Os10g0556900'
  109. 'Os10g0115600'
  110. 'Os10g0167300'
  111. 'Os10g0195100'
  112. 'Os10g0213800'
  113. 'Os10g0316400'
  114. 'Os10g0370800'
  115. 'Os10g0382400'
  116. 'Os10g0389800'
  117. 'Os10g0397200'
  118. 'Os10g0420900'
  119. 'Os10g0446600'
  120. 'Os10g0446800'
  121. 'None'
  122. 'Os10g0513200'
  123. 'Os10g0552600'
  124. 'Os10g0552800'
  125. 'Os10g0573700'
  126. 'Os11g0101200'
  127. 'Os11g0102200'
  128. 'Os11g0102400'
  129. 'Os11g0104900'
  130. 'Os11g0107000'
  131. 'Os11g0153800'
  132. 'Os11g0170400'
  133. 'Os11g0227200'
  134. 'Os11g0247300'
  135. 'Os11g0266500'
  136. 'Os11g0272800'
  137. 'Os11g0425800'
  138. 'Os11g0446000'
  139. 'Os11g0452400'
  140. 'Os11g0455800'
  141. 'Os11g0655000'
  142. 'Os11g0672300'
  143. 'Os11g0676500'
  144. 'Os11g0678000'
  145. 'Os11g0696600'
  146. 'Os11g0104400'
  147. 'Os11g0139700'
  148. 'Os11g0147800'
  149. 'Os11g0167800'
  150. 'Os11g0169900'
  151. 'Os11g0184900'
  152. 'Os11g0245500'
  153. 'Os11g0251400'
  154. 'Os11g0307600'
  155. 'Os11g0308100'
  156. 'Os11g0308600'
  157. 'Os11g0414000'
  158. 'Os11g0496600'
  159. 'Os11g0521900'
  160. 'Os11g0544200'
  161. 'Os11g0545000'
  162. 'None'
  163. 'Os11g0573000'
  164. 'Os11g0609500'
  165. 'Os11g0636900'
  166. 'Os11g0648100'
  167. 'Os12g0101800'
  168. 'Os12g0120400'
  169. 'Os12g0152800'
  170. 'Os12g0174000'
  171. 'Os12g0175700'
  172. 'Os12g0197200'
  173. 'Os12g0236700'
  174. 'Os12g0264500'
  175. 'Os12g0285100'
  176. 'Os12g0297400'
  177. 'Os12g0416500'
  178. 'Os12g0443500'
  179. 'Os12g0489100'
  180. 'None'
  181. 'None'
  182. 'None'
  183. 'None'
  184. 'Os12g0560900'
  185. 'Os12g0569700'
  186. 'Os12g0601400'
  187. 'Os12g0624000'
  188. 'Os12g0632000'
  189. 'Os12g0638700'
  190. 'Os12g0118800'
  191. 'Os12g0124100'
  192. 'None'
  193. 'Os12g0239900'
  194. 'Os12g0250900'
  195. 'None'
  196. 'Os12g0254400'
  197. 'Os12g0278800'
  198. 'Os12g0290600'
  199. 'Os12g0299300'
  200. 'None'
  201. ⋯
  202. 'Os05g0376300'
  203. 'Os05g0386800'
  204. 'Os05g0391600'
  205. 'Os05g0414501'
  206. 'Os05g0426200'
  207. 'Os05g0435500'
  208. 'Os05g0437300'
  209. 'Os05g0477300'
  210. 'Os05g0480400'
  211. 'Os05g0486700'
  212. 'Os05g0487600'
  213. 'Os05g0511400'
  214. 'Os05g0539800'
  215. 'Os05g0543400'
  216. 'Os05g0559900'
  217. 'Os05g0580550'
  218. 'Os05g0584600'
  219. 'Os05g0592600'
  220. 'Os05g0593800'
  221. 'Os05g0596600'
  222. 'Os05g0597100'
  223. 'Os06g0102300'
  224. 'Os06g0116100'
  225. 'Os06g0135000'
  226. 'Os06g0178900'
  227. 'Os06g0192900'
  228. 'Os06g0226000'
  229. 'Os06g0255200'
  230. 'None'
  231. 'Os06g0335900'
  232. 'Os06g0336200'
  233. 'Os06g0342750'
  234. 'Os06g0347100'
  235. 'Os06g0573600'
  236. 'Os06g0597200'
  237. 'None'
  238. 'Os06g0638000'
  239. 'Os06g0646500'
  240. 'Os06g0649600'
  241. 'Os06g0654300'
  242. 'Os06g0660200'
  243. 'Os06g0673700'
  244. 'Os06g0693200'
  245. 'Os06g0702500'
  246. 'Os06g0727200'
  247. 'Os06g0104400'
  248. 'Os06g0127800'
  249. 'Os06g0137100'
  250. 'Os06g0153400'
  251. 'Os06g0166500'
  252. 'Os06g0186600'
  253. 'Os06g0222400'
  254. 'Os06g0228200'
  255. 'Os06g0232100'
  256. 'Os06g0268800'
  257. 'Os06g0280900'
  258. 'Os06g0346100'
  259. 'Os06g0353400'
  260. 'Os06g0360600'
  261. 'Os06g0475500'
  262. 'Os06g0488600'
  263. 'Os06g0492000'
  264. 'Os06g0505302'
  265. 'Os06g0506200'
  266. 'Os06g0563000'
  267. 'Os06g0568200'
  268. 'Os06g0639100'
  269. 'Os06g0647700'
  270. 'Os06g0648200'
  271. 'Os06g0656500'
  272. 'Os06g0682800'
  273. 'Os06g0701100'
  274. 'Os06g0716700'
  275. 'Os06g0731800'
  276. 'Os07g0110000'
  277. 'Os07g0138100'
  278. 'Os07g0231500'
  279. 'Os07g0231800'
  280. 'Os07g0238700'
  281. 'Os07g0246200'
  282. 'Os07g0252400'
  283. 'Os07g0264900'
  284. 'Os07g0406600'
  285. 'Os07g0472500'
  286. 'Os07g0499300'
  287. 'Os07g0510200'
  288. 'Os07g0529700'
  289. 'Os07g0542900'
  290. 'Os07g0572800'
  291. 'Os07g0632600'
  292. 'Os07g0647500'
  293. 'Os07g0676900'
  294. 'Os07g0695100'
  295. 'Os07g0164300'
  296. 'Os07g0176500'
  297. 'Os07g0193600'
  298. 'Os07g0202100'
  299. 'Os07g0236200'
  300. 'None'
  301. 'None'
  302. 'Os07g0421200'
  303. 'Os07g0454400'
  304. 'Os07g0492000'
  305. 'Os07g0495200'
  306. 'Os07g0516500'
  307. 'Os07g0559400'
  308. 'Os07g0564700'
  309. 'Os07g0597400'
  310. 'Os07g0606900'
  311. 'Os07g0634400'
  312. 'Os07g0661500'
  313. 'Os07g0680300'
  314. 'Os07g0682400'
  315. 'Os07g0693600'
  316. 'Os08g0110800'
  317. 'Os08g0113100'
  318. 'Os08g0126300'
  319. 'Os08g0129800'
  320. 'Os08g0137100'
  321. 'Os08g0167000'
  322. 'Os08g0191433'
  323. 'Os08g0215200'
  324. 'Os08g0215300'
  325. 'Os08g0239300'
  326. 'Os08g0246300'
  327. 'Os08g0246400'
  328. 'Os08g0246700'
  329. 'Os08g0265500'
  330. 'Os08g0288000'
  331. 'Os08g0292000'
  332. 'Os08g0314800'
  333. 'Os08g0385400'
  334. 'Os08g0398300'
  335. 'Os08g0427700'
  336. 'Os08g0431700'
  337. 'Os08g0434500'
  338. 'Os08g0490000'
  339. 'Os08g0493800'
  340. 'Os08g0117200'
  341. 'Os08g0144400'
  342. 'Os08g0160500'
  343. 'Os08g0176900'
  344. 'Os08g0184600'
  345. 'Os08g0184800'
  346. 'Os08g0192900'
  347. 'Os08g0220600'
  348. 'Os08g0242900'
  349. 'Os08g0276000'
  350. 'Os08g0300200'
  351. 'Os08g0309300'
  352. 'Os08g0318500'
  353. 'Os08g0321000'
  354. 'Os08g0416400'
  355. 'Os08g0427900'
  356. 'Os08g0430500'
  357. 'Os08g0436800'
  358. 'Os08g0441500'
  359. 'Os08g0449500'
  360. 'Os08g0478200'
  361. 'Os08g0480100'
  362. 'Os08g0532300'
  363. 'Os08g0544500'
  364. 'Os08g0547500'
  365. 'None'
  366. 'None'
  367. 'Os09g0114500'
  368. 'Os09g0129301'
  369. 'Os09g0129400'
  370. 'Os09g0241700'
  371. 'None'
  372. 'None'
  373. 'Os09g0266400'
  374. 'Os09g0300800'
  375. 'Os09g0340400'
  376. 'Os09g0361400'
  377. 'Os09g0369000'
  378. 'Os09g0410300'
  379. 'Os09g0439050'
  380. 'Os09g0475400'
  381. 'Os09g0484200'
  382. 'Os09g0494200'
  383. 'Os09g0568400'
  384. 'Os09g0115400'
  385. 'Os09g0131400'
  386. 'Os09g0247700'
  387. 'None'
  388. 'Os09g0272900'
  389. 'Os09g0315050'
  390. 'Os09g0358000'
  391. 'Os09g0385300'
  392. 'Os09g0392666'
  393. 'Os09g0427300'
  394. 'None'
  395. 'Os09g0453100'
  396. 'Os09g0469400'
  397. 'Os09g0482780'
  398. 'Os09g0485900'
  399. 'Os09g0487100'
  400. 'Os09g0542000'
  401. 'Os09g0560900'
In [141]:
# filter out the "None" value
markers_list_all3 <- markers_list_all2
for (i in 1:length(markers_list_all3)){
    markers_list_all3[[i]] <- markers_list_all3[[i]][grep("Os",markers_list_all3[[i]])]
}
markers_list_all3[[1]]
  1. 'Os01g0101600'
  2. 'Os01g0105400'
  3. 'Os01g0118300'
  4. 'Os01g0185500'
  5. 'Os01g0191500'
  6. 'Os01g0193900'
  7. 'Os01g0208700'
  8. 'Os01g0212400'
  9. 'Os01g0214300'
  10. 'Os01g0218032'
  11. 'Os01g0263300'
  12. 'Os01g0357100'
  13. 'Os01g0386700'
  14. 'Os01g0392800'
  15. 'Os01g0539400'
  16. 'Os01g0541000'
  17. 'Os01g0543000'
  18. 'Os01g0559900'
  19. 'Os01g0563000'
  20. 'Os01g0588100'
  21. 'Os01g0591300'
  22. 'Os01g0611000'
  23. 'Os01g0649100'
  24. 'Os01g0659200'
  25. 'Os01g0685800'
  26. 'Os01g0687300'
  27. 'Os01g0723400'
  28. 'Os01g0728400'
  29. 'Os01g0734200'
  30. 'Os01g0757400'
  31. 'Os01g0772700'
  32. 'Os01g0777000'
  33. 'Os01g0798100'
  34. 'Os01g0837300'
  35. 'Os01g0855900'
  36. 'Os01g0859400'
  37. 'Os01g0876500'
  38. 'Os01g0896800'
  39. 'Os01g0897600'
  40. 'Os01g0899387'
  41. 'Os01g0900800'
  42. 'Os01g0908200'
  43. 'Os01g0911200'
  44. 'Os01g0922800'
  45. 'Os01g0927600'
  46. 'Os01g0930200'
  47. 'Os01g0944200'
  48. 'Os01g0975300'
  49. 'Os01g0978000'
  50. 'Os01g0104900'
  51. 'Os01g0109700'
  52. 'Os01g0119050'
  53. 'Os01g0120300'
  54. 'Os01g0147900'
  55. 'Os01g0169800'
  56. 'Os01g0170500'
  57. 'Os01g0182600'
  58. 'Os01g0188900'
  59. 'Os01g0195200'
  60. 'Os01g0203800'
  61. 'Os01g0256500'
  62. 'Os01g0284500'
  63. 'Os01g0291500'
  64. 'Os01g0323600'
  65. 'Os01g0328400'
  66. 'Os01g0337600'
  67. 'Os01g0361000'
  68. 'Os01g0362100'
  69. 'Os01g0612600'
  70. 'Os01g0646700'
  71. 'Os01g0668100'
  72. 'Os01g0709500'
  73. 'Os01g0716200'
  74. 'Os01g0767000'
  75. 'Os01g0775100'
  76. 'Os01g0814200'
  77. 'Os01g0816400'
  78. 'Os01g0864700'
  79. 'Os01g0889200'
  80. 'Os01g0899500'
  81. 'Os01g0901000'
  82. 'Os01g0905800'
  83. 'Os01g0916800'
  84. 'Os01g0923700'
  85. 'Os01g0933400'
  86. 'Os01g0937400'
  87. 'Os01g0961600'
  88. 'Os01g0966000'
  89. 'Os10g0132700'
  90. 'Os10g0167700'
  91. 'Os10g0172600'
  92. 'Os10g0185200'
  93. 'Os10g0204300'
  94. 'Os10g0320400'
  95. 'Os10g0394400'
  96. 'Os10g0412600'
  97. 'Os10g0431000'
  98. 'Os10g0437000'
  99. 'Os10g0454200'
  100. 'Os10g0478200'
  101. 'Os10g0493600'
  102. 'Os10g0501500'
  103. 'Os10g0536400'
  104. 'Os10g0546100'
  105. 'Os10g0556100'
  106. 'Os10g0556900'
  107. 'Os10g0115600'
  108. 'Os10g0167300'
  109. 'Os10g0195100'
  110. 'Os10g0213800'
  111. 'Os10g0316400'
  112. 'Os10g0370800'
  113. 'Os10g0382400'
  114. 'Os10g0389800'
  115. 'Os10g0397200'
  116. 'Os10g0420900'
  117. 'Os10g0446600'
  118. 'Os10g0446800'
  119. 'Os10g0513200'
  120. 'Os10g0552600'
  121. 'Os10g0552800'
  122. 'Os10g0573700'
  123. 'Os11g0101200'
  124. 'Os11g0102200'
  125. 'Os11g0102400'
  126. 'Os11g0104900'
  127. 'Os11g0107000'
  128. 'Os11g0153800'
  129. 'Os11g0170400'
  130. 'Os11g0227200'
  131. 'Os11g0247300'
  132. 'Os11g0266500'
  133. 'Os11g0272800'
  134. 'Os11g0425800'
  135. 'Os11g0446000'
  136. 'Os11g0452400'
  137. 'Os11g0455800'
  138. 'Os11g0655000'
  139. 'Os11g0672300'
  140. 'Os11g0676500'
  141. 'Os11g0678000'
  142. 'Os11g0696600'
  143. 'Os11g0104400'
  144. 'Os11g0139700'
  145. 'Os11g0147800'
  146. 'Os11g0167800'
  147. 'Os11g0169900'
  148. 'Os11g0184900'
  149. 'Os11g0245500'
  150. 'Os11g0251400'
  151. 'Os11g0307600'
  152. 'Os11g0308100'
  153. 'Os11g0308600'
  154. 'Os11g0414000'
  155. 'Os11g0496600'
  156. 'Os11g0521900'
  157. 'Os11g0544200'
  158. 'Os11g0545000'
  159. 'Os11g0573000'
  160. 'Os11g0609500'
  161. 'Os11g0636900'
  162. 'Os11g0648100'
  163. 'Os12g0101800'
  164. 'Os12g0120400'
  165. 'Os12g0152800'
  166. 'Os12g0174000'
  167. 'Os12g0175700'
  168. 'Os12g0197200'
  169. 'Os12g0236700'
  170. 'Os12g0264500'
  171. 'Os12g0285100'
  172. 'Os12g0297400'
  173. 'Os12g0416500'
  174. 'Os12g0443500'
  175. 'Os12g0489100'
  176. 'Os12g0560900'
  177. 'Os12g0569700'
  178. 'Os12g0601400'
  179. 'Os12g0624000'
  180. 'Os12g0632000'
  181. 'Os12g0638700'
  182. 'Os12g0118800'
  183. 'Os12g0124100'
  184. 'Os12g0239900'
  185. 'Os12g0250900'
  186. 'Os12g0254400'
  187. 'Os12g0278800'
  188. 'Os12g0290600'
  189. 'Os12g0299300'
  190. 'Os12g0441700'
  191. 'Os12g0460800'
  192. 'Os12g0467300'
  193. 'Os12g0503000'
  194. 'Os12g0530000'
  195. 'Os12g0535400'
  196. 'Os12g0561000'
  197. 'Os12g0568200'
  198. 'Os12g0583500'
  199. 'Os12g0590500'
  200. 'Os12g0600701'
  201. ⋯
  202. 'Os05g0148000'
  203. 'Os05g0151000'
  204. 'Os05g0152201'
  205. 'Os05g0199100'
  206. 'Os05g0202500'
  207. 'Os05g0243200'
  208. 'Os05g0295300'
  209. 'Os05g0320700'
  210. 'Os05g0335401'
  211. 'Os05g0363200'
  212. 'Os05g0376300'
  213. 'Os05g0386800'
  214. 'Os05g0391600'
  215. 'Os05g0414501'
  216. 'Os05g0426200'
  217. 'Os05g0435500'
  218. 'Os05g0437300'
  219. 'Os05g0477300'
  220. 'Os05g0480400'
  221. 'Os05g0486700'
  222. 'Os05g0487600'
  223. 'Os05g0511400'
  224. 'Os05g0539800'
  225. 'Os05g0543400'
  226. 'Os05g0559900'
  227. 'Os05g0580550'
  228. 'Os05g0584600'
  229. 'Os05g0592600'
  230. 'Os05g0593800'
  231. 'Os05g0596600'
  232. 'Os05g0597100'
  233. 'Os06g0102300'
  234. 'Os06g0116100'
  235. 'Os06g0135000'
  236. 'Os06g0178900'
  237. 'Os06g0192900'
  238. 'Os06g0226000'
  239. 'Os06g0255200'
  240. 'Os06g0335900'
  241. 'Os06g0336200'
  242. 'Os06g0342750'
  243. 'Os06g0347100'
  244. 'Os06g0573600'
  245. 'Os06g0597200'
  246. 'Os06g0638000'
  247. 'Os06g0646500'
  248. 'Os06g0649600'
  249. 'Os06g0654300'
  250. 'Os06g0660200'
  251. 'Os06g0673700'
  252. 'Os06g0693200'
  253. 'Os06g0702500'
  254. 'Os06g0727200'
  255. 'Os06g0104400'
  256. 'Os06g0127800'
  257. 'Os06g0137100'
  258. 'Os06g0153400'
  259. 'Os06g0166500'
  260. 'Os06g0186600'
  261. 'Os06g0222400'
  262. 'Os06g0228200'
  263. 'Os06g0232100'
  264. 'Os06g0268800'
  265. 'Os06g0280900'
  266. 'Os06g0346100'
  267. 'Os06g0353400'
  268. 'Os06g0360600'
  269. 'Os06g0475500'
  270. 'Os06g0488600'
  271. 'Os06g0492000'
  272. 'Os06g0505302'
  273. 'Os06g0506200'
  274. 'Os06g0563000'
  275. 'Os06g0568200'
  276. 'Os06g0639100'
  277. 'Os06g0647700'
  278. 'Os06g0648200'
  279. 'Os06g0656500'
  280. 'Os06g0682800'
  281. 'Os06g0701100'
  282. 'Os06g0716700'
  283. 'Os06g0731800'
  284. 'Os07g0110000'
  285. 'Os07g0138100'
  286. 'Os07g0231500'
  287. 'Os07g0231800'
  288. 'Os07g0238700'
  289. 'Os07g0246200'
  290. 'Os07g0252400'
  291. 'Os07g0264900'
  292. 'Os07g0406600'
  293. 'Os07g0472500'
  294. 'Os07g0499300'
  295. 'Os07g0510200'
  296. 'Os07g0529700'
  297. 'Os07g0542900'
  298. 'Os07g0572800'
  299. 'Os07g0632600'
  300. 'Os07g0647500'
  301. 'Os07g0676900'
  302. 'Os07g0695100'
  303. 'Os07g0164300'
  304. 'Os07g0176500'
  305. 'Os07g0193600'
  306. 'Os07g0202100'
  307. 'Os07g0236200'
  308. 'Os07g0421200'
  309. 'Os07g0454400'
  310. 'Os07g0492000'
  311. 'Os07g0495200'
  312. 'Os07g0516500'
  313. 'Os07g0559400'
  314. 'Os07g0564700'
  315. 'Os07g0597400'
  316. 'Os07g0606900'
  317. 'Os07g0634400'
  318. 'Os07g0661500'
  319. 'Os07g0680300'
  320. 'Os07g0682400'
  321. 'Os07g0693600'
  322. 'Os08g0110800'
  323. 'Os08g0113100'
  324. 'Os08g0126300'
  325. 'Os08g0129800'
  326. 'Os08g0137100'
  327. 'Os08g0167000'
  328. 'Os08g0191433'
  329. 'Os08g0215200'
  330. 'Os08g0215300'
  331. 'Os08g0239300'
  332. 'Os08g0246300'
  333. 'Os08g0246400'
  334. 'Os08g0246700'
  335. 'Os08g0265500'
  336. 'Os08g0288000'
  337. 'Os08g0292000'
  338. 'Os08g0314800'
  339. 'Os08g0385400'
  340. 'Os08g0398300'
  341. 'Os08g0427700'
  342. 'Os08g0431700'
  343. 'Os08g0434500'
  344. 'Os08g0490000'
  345. 'Os08g0493800'
  346. 'Os08g0117200'
  347. 'Os08g0144400'
  348. 'Os08g0160500'
  349. 'Os08g0176900'
  350. 'Os08g0184600'
  351. 'Os08g0184800'
  352. 'Os08g0192900'
  353. 'Os08g0220600'
  354. 'Os08g0242900'
  355. 'Os08g0276000'
  356. 'Os08g0300200'
  357. 'Os08g0309300'
  358. 'Os08g0318500'
  359. 'Os08g0321000'
  360. 'Os08g0416400'
  361. 'Os08g0427900'
  362. 'Os08g0430500'
  363. 'Os08g0436800'
  364. 'Os08g0441500'
  365. 'Os08g0449500'
  366. 'Os08g0478200'
  367. 'Os08g0480100'
  368. 'Os08g0532300'
  369. 'Os08g0544500'
  370. 'Os08g0547500'
  371. 'Os09g0114500'
  372. 'Os09g0129301'
  373. 'Os09g0129400'
  374. 'Os09g0241700'
  375. 'Os09g0266400'
  376. 'Os09g0300800'
  377. 'Os09g0340400'
  378. 'Os09g0361400'
  379. 'Os09g0369000'
  380. 'Os09g0410300'
  381. 'Os09g0439050'
  382. 'Os09g0475400'
  383. 'Os09g0484200'
  384. 'Os09g0494200'
  385. 'Os09g0568400'
  386. 'Os09g0115400'
  387. 'Os09g0131400'
  388. 'Os09g0247700'
  389. 'Os09g0272900'
  390. 'Os09g0315050'
  391. 'Os09g0358000'
  392. 'Os09g0385300'
  393. 'Os09g0392666'
  394. 'Os09g0427300'
  395. 'Os09g0453100'
  396. 'Os09g0469400'
  397. 'Os09g0482780'
  398. 'Os09g0485900'
  399. 'Os09g0487100'
  400. 'Os09g0542000'
  401. 'Os09g0560900'
In [142]:
# Run GO term analysis with gprofiler2 gost function
cluster_GO_all <- gost(markers_list_all3, organism = "osativa", correction_method = "fdr", significant = FALSE, multi_query = FALSE)

cluster_GO_all_df <- cluster_GO_all[[1]]

cluster_GO_all_sig <- filter(cluster_GO_all_df, p_value<=0.01)
head(cluster_GO_all_sig, n=5)
A data.frame: 5 × 14
querysignificantp_valueterm_sizequery_sizeintersection_sizeprecisionrecallterm_idsourceterm_nameeffective_domain_sizesource_orderparents
<chr><lgl><dbl><int><int><int><dbl><dbl><chr><chr><chr><int><int><list>
1AtrichoblastTRUE0.002319737120358130.036312850.10833333GO:0009205GO:BPpurine ribonucleoside triphosphate metabolic process15948 3408GO:00091....
2AtrichoblastTRUE0.002319737121358130.036312850.10743802GO:0009144GO:BPpurine nucleoside triphosphate metabolic process 15948 3348 GO:0009141
3AtrichoblastTRUE0.003422468132358130.036312850.09848485GO:0009199GO:BPribonucleoside triphosphate metabolic process 15948 3402 GO:0009141
4AtrichoblastTRUE0.003422468114358120.033519550.10526316GO:0046034GO:BPATP metabolic process 1594812209GO:00091....
5AtrichoblastTRUE0.004201293140358130.036312850.09285714GO:0009141GO:BPnucleoside triphosphate metabolic process 15948 3345 GO:0006753
In [143]:
# Save the GO term analysis result
cluster_GO_all_save <- as.matrix (cluster_GO_all_sig)
write.csv(cluster_GO_all_save, file = "./1-DE_analysis/snRNA-seq_CMPvsGel_DE-combined_gene_GO_analysis.csv", row.names = TRUE)
In [144]:
# Save the GO term analysis result
cluster_GO_all_df <- as.matrix (cluster_GO_all_df)
write.csv(cluster_GO_all_df, file = "./1-DE_analysis/snRNA-seq_CMPvsGel_DE-combined_gene_GO_analysis-full.csv", row.names = TRUE)
In [ ]:

GO term analysis with gprofiler2¶

In [106]:
## GO term analysis for DEGs
# 
markers_sel <- select(tb2_fil, gene, clust_up_dn)

markers_list <- split(markers_sel, f=markers_sel$clust_up_dn)
 
#this makes list from long df of gene lists - TARGET is what we want to keep
markers_list  <- lapply(markers_list, function(x) x[names(x)=="gene"])
# convert each sublist into character and eliminate duplicates
markers_list  <- lapply(markers_list, function(x) as.character(unique(x$gene)))
In [130]:
head(tb2_fil)
A data.frame: 6 × 17
genecluster_idsc_297.frqsc_298.frqsc_301.frqsc_302.frqgel.frqsoil.frqlogFClogCPMFp_valp_adj.locp_adj.glbcontrastup_dn_labelclust_up_dn
<chr><chr><dbl><dbl><dbl><dbl><dbl><dbl><dbl><dbl><dbl><dbl><dbl><dbl><chr><chr><chr>
1LOC-Os01g01150Meristem0.13700.1740.003630.004920.1510.004131.4704.6316.106.13e-050.001490.00251gel-soilDownMeristem_Down
2LOC-Os01g01450Meristem0.11400.1250.004150.002460.1180.003491.3204.2710.601.13e-030.016500.02580gel-soilDownMeristem_Down
3LOC-Os01g01510Meristem0.15600.2020.008290.005740.1740.007310.8494.92 8.363.83e-030.042200.06310gel-soilDownMeristem_Down
4LOC-Os01g01570Meristem0.15100.2230.003630.009840.1790.006041.2404.9415.707.58e-050.001790.00300gel-soilDownMeristem_Down
5LOC-Os01g02890Meristem0.09520.1200.002590.002460.1050.002541.5904.0812.005.36e-040.009100.01440gel-soilDownMeristem_Down
6LOC-Os01g06010Meristem0.11400.1350.004670.003280.1220.004131.0304.44 8.164.28e-030.045900.06830gel-soilDownMeristem_Down
In [107]:
length(markers_list)
22
In [108]:
# Change the format of gene ID to make it recognizable: change"-" to "_"
for (i in 1:length(markers_list)){
    markers_list[[i]] <- gsub("LOC-","LOC_",markers_list[[i]])
} 
head(markers_list, n=1)
$Atrichoblast_Down =
  1. 'LOC_Os01g01150'
  2. 'LOC_Os01g01570'
  3. 'LOC_Os01g02890'
  4. 'LOC_Os01g09030'
  5. 'LOC_Os01g09760'
  6. 'LOC_Os01g11054'
  7. 'LOC_Os01g11414'
  8. 'LOC_Os01g11580'
  9. 'LOC_Os01g11900'
  10. 'LOC_Os01g15830'
  11. 'LOC_Os01g25484'
  12. 'LOC_Os01g28989'
  13. 'LOC_Os01g29820'
  14. 'LOC_Os01g35789'
  15. 'LOC_Os01g35930'
  16. 'LOC_Os01g36229'
  17. 'LOC_Os01g37950'
  18. 'LOC_Os01g38229'
  19. 'LOC_Os01g40560'
  20. 'LOC_Os01g40870'
  21. 'LOC_Os01g42520'
  22. 'LOC_Os01g49310'
  23. 'LOC_Os01g52810'
  24. 'LOC_Os01g53294'
  25. 'LOC_Os01g55260'
  26. 'LOC_Os01g56590'
  27. 'LOC_Os01g56910'
  28. 'LOC_Os01g58459'
  29. 'LOC_Os01g62020'
  30. 'LOC_Os01g63710'
  31. 'LOC_Os01g64010'
  32. 'LOC_Os01g65530'
  33. 'LOC_Os01g67134'
  34. 'LOC_Os01g67220'
  35. 'LOC_Os01g67480'
  36. 'LOC_Os01g68020'
  37. 'LOC_Os01g68324'
  38. 'LOC_Os01g69850'
  39. 'LOC_Os01g70270'
  40. 'LOC_Os01g70470'
  41. 'LOC_Os01g71630'
  42. 'LOC_Os01g74640'
  43. 'LOC_Os01g01520'
  44. 'LOC_Os01g01960'
  45. 'LOC_Os01g02940'
  46. 'LOC_Os01g03020'
  47. 'LOC_Os01g07500'
  48. 'LOC_Os01g07570'
  49. 'LOC_Os01g08700'
  50. 'LOC_Os01g09370'
  51. 'LOC_Os01g09860'
  52. 'LOC_Os01g10680'
  53. 'LOC_Os01g18170'
  54. 'LOC_Os01g18744'
  55. 'LOC_Os01g22010'
  56. 'LOC_Os01g23590'
  57. 'LOC_Os01g25920'
  58. 'LOC_Os01g26039'
  59. 'LOC_Os01g42700'
  60. 'LOC_Os01g45880'
  61. 'LOC_Os01g47780'
  62. 'LOC_Os01g51290'
  63. 'LOC_Os01g51840'
  64. 'LOC_Os01g56140'
  65. 'LOC_Os01g56780'
  66. 'LOC_Os01g59880'
  67. 'LOC_Os01g60040'
  68. 'LOC_Os01g64490'
  69. 'LOC_Os01g66580'
  70. 'LOC_Os01g67370'
  71. 'LOC_Os01g67500'
  72. 'LOC_Os01g68810'
  73. 'LOC_Os01g69920'
  74. 'LOC_Os01g70720'
  75. 'LOC_Os01g71114'
  76. 'LOC_Os01g73080'
  77. 'LOC_Os01g73514'
  78. 'LOC_Os10g04342'
  79. 'LOC_Os10g08599'
  80. 'LOC_Os10g09200'
  81. 'LOC_Os10g10580'
  82. 'LOC_Os10g13694'
  83. 'LOC_Os10g25487'
  84. 'LOC_Os10g27274'
  85. 'LOC_Os10g29560'
  86. 'LOC_Os10g30080'
  87. 'LOC_Os10g31660'
  88. 'LOC_Os10g35110'
  89. 'LOC_Os10g35770'
  90. 'LOC_Os10g39140'
  91. 'LOC_Os10g39890'
  92. 'LOC_Os10g40730'
  93. 'LOC_Os10g40790'
  94. 'LOC_Os10g02630'
  95. 'LOC_Os10g11870'
  96. 'LOC_Os10g15310'
  97. 'LOC_Os10g16640'
  98. 'LOC_Os10g22570'
  99. 'LOC_Os10g24094'
  100. 'LOC_Os10g25090'
  101. 'LOC_Os10g25770'
  102. 'LOC_Os10g28510'
  103. 'LOC_Os10g30951'
  104. 'LOC_Os10g30970'
  105. 'LOC_Os10g31730'
  106. 'LOC_Os10g36924'
  107. 'LOC_Os10g42299'
  108. 'LOC_Os11g01074'
  109. 'LOC_Os11g01154'
  110. 'LOC_Os11g01380'
  111. 'LOC_Os11g01570'
  112. 'LOC_Os11g05562'
  113. 'LOC_Os11g12000'
  114. 'LOC_Os11g16530'
  115. 'LOC_Os11g17290'
  116. 'LOC_Os11g23880'
  117. 'LOC_Os11g25920'
  118. 'LOC_Os11g26594'
  119. 'LOC_Os11g26860'
  120. 'LOC_Os11g43404'
  121. 'LOC_Os11g44870'
  122. 'LOC_Os11g45130'
  123. 'LOC_Os11g45280'
  124. 'LOC_Os11g47370'
  125. 'LOC_Os11g01340'
  126. 'LOC_Os11g04409'
  127. 'LOC_Os11g05050'
  128. 'LOC_Os11g08210'
  129. 'LOC_Os11g14070'
  130. 'LOC_Os11g20239'
  131. 'LOC_Os11g20310'
  132. 'LOC_Os11g20330'
  133. 'LOC_Os11g30370'
  134. 'LOC_Os11g31890'
  135. 'LOC_Os11g34150'
  136. 'LOC_Os11g34230'
  137. 'LOC_Os11g34650'
  138. 'LOC_Os11g36470'
  139. 'LOC_Os11g39530'
  140. 'LOC_Os11g41820'
  141. 'LOC_Os11g42800'
  142. 'LOC_Os12g02750'
  143. 'LOC_Os12g05660'
  144. 'LOC_Os12g07530'
  145. 'LOC_Os12g07670'
  146. 'LOC_Os12g09550'
  147. 'LOC_Os12g13440'
  148. 'LOC_Os12g16350'
  149. 'LOC_Os12g18729'
  150. 'LOC_Os12g20144'
  151. 'LOC_Os12g22760'
  152. 'LOC_Os12g25690'
  153. 'LOC_Os12g30540'
  154. 'LOC_Os12g32536'
  155. 'LOC_Os12g38180'
  156. 'LOC_Os12g40900'
  157. 'LOC_Os12g42884'
  158. 'LOC_Os12g43600'
  159. 'LOC_Os12g44150'
  160. 'LOC_Os12g02660'
  161. 'LOC_Os12g03080'
  162. 'LOC_Os12g06040'
  163. 'LOC_Os12g13720'
  164. 'LOC_Os12g14840'
  165. 'LOC_Os12g14930'
  166. 'LOC_Os12g15222'
  167. 'LOC_Os12g19350'
  168. 'LOC_Os12g20390'
  169. 'LOC_Os12g23570'
  170. 'LOC_Os12g25494'
  171. 'LOC_Os12g27520'
  172. 'LOC_Os12g28100'
  173. 'LOC_Os12g31860'
  174. 'LOC_Os12g34092'
  175. 'LOC_Os12g34510'
  176. 'LOC_Os12g34990'
  177. 'LOC_Os12g39380'
  178. 'LOC_Os12g39980'
  179. 'LOC_Os12g40840'
  180. 'LOC_Os12g40890'
  181. 'LOC_Os12g41430'
  182. 'LOC_Os12g41820'
  183. 'LOC_Os12g41900'
  184. 'LOC_Os12g42400'
  185. 'LOC_Os12g44330'
  186. 'LOC_Os12g44360'
  187. 'LOC_Os12g44390'
  188. 'LOC_Os02g03840'
  189. 'LOC_Os02g04680'
  190. 'LOC_Os02g05199'
  191. 'LOC_Os02g05630'
  192. 'LOC_Os02g06592'
  193. 'LOC_Os02g07010'
  194. 'LOC_Os02g07340'
  195. 'LOC_Os02g08100'
  196. 'LOC_Os02g08360'
  197. 'LOC_Os02g10650'
  198. 'LOC_Os02g13130'
  199. 'LOC_Os02g14900'
  200. 'LOC_Os02g20950'
  201. ⋯
  202. 'LOC_Os04g41970'
  203. 'LOC_Os04g43760'
  204. 'LOC_Os04g47240'
  205. 'LOC_Os04g52020'
  206. 'LOC_Os04g52370'
  207. 'LOC_Os04g52590'
  208. 'LOC_Os04g54930'
  209. 'LOC_Os04g57860'
  210. 'LOC_Os04g58504'
  211. 'LOC_Os04g59150'
  212. 'LOC_Os05g03174'
  213. 'LOC_Os05g04380'
  214. 'LOC_Os05g04510'
  215. 'LOC_Os05g06470'
  216. 'LOC_Os05g07600'
  217. 'LOC_Os05g12300'
  218. 'LOC_Os05g22830'
  219. 'LOC_Os05g25770'
  220. 'LOC_Os05g26040'
  221. 'LOC_Os05g36960'
  222. 'LOC_Os05g44400'
  223. 'LOC_Os05g46954'
  224. 'LOC_Os05g48040'
  225. 'LOC_Os05g48960'
  226. 'LOC_Os05g01910'
  227. 'LOC_Os05g02130'
  228. 'LOC_Os05g02310'
  229. 'LOC_Os05g03040'
  230. 'LOC_Os05g03550'
  231. 'LOC_Os05g05530'
  232. 'LOC_Os05g05860'
  233. 'LOC_Os05g06014'
  234. 'LOC_Os05g11260'
  235. 'LOC_Os05g15220'
  236. 'LOC_Os05g15360'
  237. 'LOC_Os05g22940'
  238. 'LOC_Os05g25640'
  239. 'LOC_Os05g26990'
  240. 'LOC_Os05g29990'
  241. 'LOC_Os05g31230'
  242. 'LOC_Os05g32110'
  243. 'LOC_Os05g32544'
  244. 'LOC_Os05g34260'
  245. 'LOC_Os05g35980'
  246. 'LOC_Os05g36120'
  247. 'LOC_Os05g40200'
  248. 'LOC_Os05g40900'
  249. 'LOC_Os05g46240'
  250. 'LOC_Os05g46580'
  251. 'LOC_Os05g48620'
  252. 'LOC_Os05g50420'
  253. 'LOC_Os05g50750'
  254. 'LOC_Os05g51560'
  255. 'LOC_Os05g51790'
  256. 'LOC_Os05g51830'
  257. 'LOC_Os06g01260'
  258. 'LOC_Os06g04399'
  259. 'LOC_Os06g08080'
  260. 'LOC_Os06g09320'
  261. 'LOC_Os06g12170'
  262. 'LOC_Os06g14406'
  263. 'LOC_Os06g21730'
  264. 'LOC_Os06g22919'
  265. 'LOC_Os06g23504'
  266. 'LOC_Os06g23870'
  267. 'LOC_Os06g37560'
  268. 'LOC_Os06g39600'
  269. 'LOC_Os06g39700'
  270. 'LOC_Os06g43120'
  271. 'LOC_Os06g44034'
  272. 'LOC_Os06g44410'
  273. 'LOC_Os06g44970'
  274. 'LOC_Os06g46149'
  275. 'LOC_Os06g48940'
  276. 'LOC_Os06g01500'
  277. 'LOC_Os06g03710'
  278. 'LOC_Os06g04560'
  279. 'LOC_Os06g07040'
  280. 'LOC_Os06g08740'
  281. 'LOC_Os06g11860'
  282. 'LOC_Os06g12310'
  283. 'LOC_Os06g12590'
  284. 'LOC_Os06g15779'
  285. 'LOC_Os06g16919'
  286. 'LOC_Os06g23770'
  287. 'LOC_Os06g24594'
  288. 'LOC_Os06g25500'
  289. 'LOC_Os06g28144'
  290. 'LOC_Os06g29380'
  291. 'LOC_Os06g29650'
  292. 'LOC_Os06g30901'
  293. 'LOC_Os06g30950'
  294. 'LOC_Os06g36740'
  295. 'LOC_Os06g43940'
  296. 'LOC_Os06g43980'
  297. 'LOC_Os06g44620'
  298. 'LOC_Os06g46890'
  299. 'LOC_Os06g50300'
  300. 'LOC_Os07g01904'
  301. 'LOC_Os07g04550'
  302. 'LOC_Os07g12780'
  303. 'LOC_Os07g12800'
  304. 'LOC_Os07g13460'
  305. 'LOC_Os07g14270'
  306. 'LOC_Os07g16140'
  307. 'LOC_Os07g22390'
  308. 'LOC_Os07g28940'
  309. 'LOC_Os07g31599'
  310. 'LOC_Os07g32600'
  311. 'LOC_Os07g34580'
  312. 'LOC_Os07g35860'
  313. 'LOC_Os07g38530'
  314. 'LOC_Os07g43870'
  315. 'LOC_Os07g47990'
  316. 'LOC_Os07g49460'
  317. 'LOC_Os07g09580'
  318. 'LOC_Os07g13234'
  319. 'LOC_Os07g23270'
  320. 'LOC_Os07g23480'
  321. 'LOC_Os07g23930'
  322. 'LOC_Os07g27140'
  323. 'LOC_Os07g33300'
  324. 'LOC_Os07g37310'
  325. 'LOC_Os07g37750'
  326. 'LOC_Os07g40640'
  327. 'LOC_Os07g41600'
  328. 'LOC_Os07g44060'
  329. 'LOC_Os07g46690'
  330. 'LOC_Os07g48410'
  331. 'LOC_Os07g49280'
  332. 'LOC_Os08g01930'
  333. 'LOC_Os08g03579'
  334. 'LOC_Os08g04270'
  335. 'LOC_Os08g07010'
  336. 'LOC_Os08g09230'
  337. 'LOC_Os08g11470'
  338. 'LOC_Os08g11480'
  339. 'LOC_Os08g14109'
  340. 'LOC_Os08g14850'
  341. 'LOC_Os08g14860'
  342. 'LOC_Os08g14880'
  343. 'LOC_Os08g16480'
  344. 'LOC_Os08g19114'
  345. 'LOC_Os08g19590'
  346. 'LOC_Os08g29615'
  347. 'LOC_Os08g30770'
  348. 'LOC_Os08g33100'
  349. 'LOC_Os08g33479'
  350. 'LOC_Os08g33740'
  351. 'LOC_Os08g38210'
  352. 'LOC_Os08g38560'
  353. 'LOC_Os08g04920'
  354. 'LOC_Os08g06380'
  355. 'LOC_Os08g07970'
  356. 'LOC_Os08g08586'
  357. 'LOC_Os08g08592'
  358. 'LOC_Os08g12430'
  359. 'LOC_Os08g14460'
  360. 'LOC_Os08g17370'
  361. 'LOC_Os08g20544'
  362. 'LOC_Os08g21760'
  363. 'LOC_Os08g22864'
  364. 'LOC_Os08g23180'
  365. 'LOC_Os08g32100'
  366. 'LOC_Os08g33120'
  367. 'LOC_Os08g34280'
  368. 'LOC_Os08g34879'
  369. 'LOC_Os08g43130'
  370. 'LOC_Os08g43400'
  371. 'LOC_Os09g02650'
  372. 'LOC_Os09g04290'
  373. 'LOC_Os09g04300'
  374. 'LOC_Os09g06634'
  375. 'LOC_Os09g07640'
  376. 'LOC_Os09g08910'
  377. 'LOC_Os09g09360'
  378. 'LOC_Os09g12970'
  379. 'LOC_Os09g17049'
  380. 'LOC_Os09g20350'
  381. 'LOC_Os09g24440'
  382. 'LOC_Os09g26770'
  383. 'LOC_Os09g29930'
  384. 'LOC_Os09g32080'
  385. 'LOC_Os09g39500'
  386. 'LOC_Os09g04504'
  387. 'LOC_Os09g07300'
  388. 'LOC_Os09g10054'
  389. 'LOC_Os09g14610'
  390. 'LOC_Os09g19350'
  391. 'LOC_Os09g21689'
  392. 'LOC_Os09g22505'
  393. 'LOC_Os09g25880'
  394. 'LOC_Os09g27744'
  395. 'LOC_Os09g27970'
  396. 'LOC_Os09g30486'
  397. 'LOC_Os09g31180'
  398. 'LOC_Os09g31220'
  399. 'LOC_Os09g37006'
  400. 'LOC_Os09g38790'
  401. 'ChrSy.fgenesh.gene.29'
In [109]:
# Remove all the gene IDs which does not follow "LOC_OS" format
for (i in 1:length(markers_list)){
    markers_list[[i]] <- markers_list[[i]][grep("LOC_",markers_list[[i]])]
}
In [110]:
# Load the MSU-RAP ID converter table downloaded from https://rapdb.dna.affrc.go.jp/download/irgsp1.html
msu2rap <- read.table("./ID_conversion/RAP-MSU_2023-03-15.txt.gz")
head(msu2rap, n=5)
A data.frame: 5 × 2
V1V2
<chr><chr>
1Os01g0100100LOC_Os01g01010.1,LOC_Os01g01010.2
2Os01g0100200LOC_Os01g01019.1
3Os01g0100300None
4Os01g0100400LOC_Os01g01030.1
5Os01g0100466None
In [111]:
# Convert the MSU ID to RAP ID if the MSU ID can be found in V2 column in msu2rap table
# grep does not require exact mtach
markers_list2 <- markers_list
for (i in 1:length(markers_list2)){
    for (j in 1:length(markers_list2[[i]])){
    suppressMessages(markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j],msu2rap$V2)])  
    } 
}
## There will be warning message because RAP and MSU are not strictly one to one

Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
Warning message in markers_list2[[i]][j] <- msu2rap$V1[grep(markers_list2[[i]][j], :
“number of items to replace is not a multiple of replacement length”
In [112]:
#Check whether conversion works
markers_list2[[14]]
  1. 'Os01g0179300'
  2. 'Os01g0191500'
  3. 'Os01g0279300'
  4. 'Os01g0649100'
  5. 'Os01g0652600'
  6. 'Os01g0659200'
  7. 'Os01g0685800'
  8. 'Os01g0686800'
  9. 'Os01g0723400'
  10. 'Os01g0815800'
  11. 'Os01g0817700'
  12. 'Os01g0823300'
  13. 'Os01g0899387'
  14. 'Os01g0147900'
  15. 'Os01g0173100'
  16. 'Os01g0231700'
  17. 'Os01g0256500'
  18. 'Os01g0290700'
  19. 'Os01g0328400'
  20. 'Os01g0332900'
  21. 'None'
  22. 'Os01g0550100'
  23. 'Os01g0550300'
  24. 'Os01g0609900'
  25. 'Os01g0654500'
  26. 'Os01g0658400'
  27. 'Os01g0666900'
  28. 'Os01g0905800'
  29. 'Os10g0320400'
  30. 'Os10g0478200'
  31. 'None'
  32. 'Os10g0167300'
  33. 'Os10g0552600'
  34. 'Os10g0552800'
  35. 'Os10g0569200'
  36. 'Os11g0102200'
  37. 'Os11g0170400'
  38. 'Os11g0220800'
  39. 'Os11g0167800'
  40. 'Os11g0169900'
  41. 'Os11g0199200'
  42. 'Os11g0244800'
  43. 'Os11g0251400'
  44. 'Os11g0414000'
  45. 'Os12g0101800'
  46. 'Os12g0167900'
  47. 'Os12g0428600'
  48. 'Os12g0502200'
  49. 'None'
  50. 'None'
  51. 'None'
  52. 'Os12g0560900'
  53. 'Os12g0278800'
  54. 'Os12g0443700'
  55. 'Os12g0514500'
  56. 'None'
  57. 'Os12g0561000'
  58. 'Os12g0568200'
  59. 'Os02g0102300'
  60. 'Os02g0105200'
  61. 'Os02g0131300'
  62. 'Os02g0170100'
  63. 'Os02g0175800'
  64. 'Os02g0274100'
  65. 'Os02g0519700'
  66. 'Os02g0519900'
  67. 'Os02g0621700'
  68. 'Os02g0745600'
  69. 'Os02g0785800'
  70. 'Os02g0101700'
  71. 'Os02g0162500'
  72. 'Os02g0200900'
  73. 'Os02g0258200'
  74. 'Os02g0287000'
  75. 'Os02g0480900'
  76. 'Os02g0572400'
  77. 'Os02g0767500'
  78. 'Os02g0787800'
  79. 'Os03g0103100'
  80. 'Os03g0139100'
  81. 'Os03g0154700'
  82. 'Os03g0227000'
  83. 'Os03g0241200'
  84. 'Os03g0273800'
  85. 'Os03g0274000'
  86. 'Os03g0297100'
  87. 'Os03g0351500'
  88. 'Os03g0356700'
  89. 'Os03g0388500'
  90. 'Os03g0390400'
  91. 'Os03g0581800'
  92. 'Os03g0606200'
  93. 'Os03g0712700'
  94. 'Os03g0741100'
  95. 'Os03g0743400'
  96. 'Os03g0758800'
  97. 'Os03g0772800'
  98. 'Os03g0796000'
  99. 'Os03g0804800'
  100. 'Os03g0806900'
  101. 'Os03g0821100'
  102. 'Os03g0136900'
  103. 'Os03g0166000'
  104. 'Os03g0234200'
  105. 'Os03g0248600'
  106. 'Os03g0254700'
  107. 'Os03g0401300'
  108. 'Os03g0407000'
  109. 'Os03g0577000'
  110. 'Os03g0586800'
  111. 'Os03g0695600'
  112. 'Os03g0742900'
  113. 'Os03g0743900'
  114. 'Os03g0794700'
  115. 'Os04g0118400'
  116. 'Os04g0418800'
  117. 'Os04g0449900'
  118. 'Os04g0486600'
  119. 'Os04g0551800'
  120. 'Os04g0584600'
  121. 'Os04g0592400'
  122. 'Os04g0432600'
  123. 'Os04g0566500'
  124. 'Os04g0601700'
  125. 'Os04g0620000'
  126. 'Os04g0660500'
  127. 'Os04g0687100'
  128. 'Os05g0105900'
  129. 'Os05g0114700'
  130. 'Os05g0143500'
  131. 'Os05g0154700'
  132. 'Os05g0160200'
  133. 'Os05g0241200'
  134. 'Os05g0317200'
  135. 'Os05g0418000'
  136. 'Os05g0420600'
  137. 'Os05g0460200'
  138. 'Os05g0481600'
  139. 'Os05g0490100'
  140. 'Os05g0498400'
  141. 'Os05g0533100'
  142. 'Os05g0556900'
  143. 'Os05g0155601'
  144. 'Os05g0160300'
  145. 'Os05g0346300'
  146. 'Os05g0455500'
  147. 'Os05g0477300'
  148. 'Os05g0482700'
  149. 'Os05g0486700'
  150. 'Os05g0503300'
  151. 'Os05g0511400'
  152. 'Os05g0553000'
  153. 'Os05g0587100'
  154. 'Os05g0592600'
  155. 'Os06g0116100'
  156. 'Os06g0336200'
  157. 'Os06g0367100'
  158. 'Os06g0574500'
  159. 'Os06g0646500'
  160. 'Os06g0693200'
  161. 'Os06g0727200'
  162. 'Os06g0728000'
  163. 'Os06g0114000'
  164. 'Os06g0153400'
  165. 'Os06g0208300'
  166. 'Os06g0247500'
  167. 'Os06g0562600'
  168. 'Os06g0568200'
  169. 'Os06g0598900'
  170. 'Os06g0639100'
  171. 'Os06g0701100'
  172. 'Os06g0730600'
  173. 'Os06g0731800'
  174. 'Os07g0176200'
  175. 'Os07g0201100'
  176. 'Os07g0448800'
  177. 'Os07g0577700'
  178. 'Os07g0615200'
  179. 'Os07g0647500'
  180. 'Os07g0675000'
  181. 'Os07g0109500'
  182. 'Os07g0134800'
  183. 'Os07g0202100'
  184. 'Os07g0407700'
  185. 'Os07g0492000'
  186. 'Os07g0495200'
  187. 'Os07g0529800'
  188. 'Os07g0691800'
  189. 'Os08g0113100'
  190. 'Os08g0126300'
  191. 'Os08g0301500'
  192. 'Os08g0314800'
  193. 'Os08g0504700'
  194. 'Os08g0559200'
  195. 'Os08g0117200'
  196. 'Os08g0191100'
  197. 'Os08g0192900'
  198. 'Os08g0295300'
  199. 'Os08g0430500'
  200. 'Os08g0436800'
  201. 'Os08g0478200'
  202. 'Os08g0480100'
  203. 'Os08g0532300'
  204. 'None'
  205. 'None'
  206. 'Os09g0361400'
  207. 'Os09g0362800'
  208. 'Os09g0434500'
  209. 'Os09g0484200'
  210. 'Os09g0492700'
  211. 'Os09g0501200'
  212. 'Os09g0509200'
  213. 'Os09g0513000'
  214. 'Os09g0553200'
  215. 'Os09g0556300'
  216. 'Os09g0115400'
  217. 'Os09g0249700'
  218. 'Os09g0258600'
  219. 'Os09g0424300'
  220. 'Os09g0467700'
  221. 'Os09g0469400'
  222. 'Os09g0568800'
In [113]:
# filter out the "None" value
markers_list3 <- markers_list2
for (i in 1:length(markers_list3)){
    markers_list3[[i]] <- markers_list3[[i]][grep("Os",markers_list3[[i]])]
}
markers_list3[[14]]
  1. 'Os01g0179300'
  2. 'Os01g0191500'
  3. 'Os01g0279300'
  4. 'Os01g0649100'
  5. 'Os01g0652600'
  6. 'Os01g0659200'
  7. 'Os01g0685800'
  8. 'Os01g0686800'
  9. 'Os01g0723400'
  10. 'Os01g0815800'
  11. 'Os01g0817700'
  12. 'Os01g0823300'
  13. 'Os01g0899387'
  14. 'Os01g0147900'
  15. 'Os01g0173100'
  16. 'Os01g0231700'
  17. 'Os01g0256500'
  18. 'Os01g0290700'
  19. 'Os01g0328400'
  20. 'Os01g0332900'
  21. 'Os01g0550100'
  22. 'Os01g0550300'
  23. 'Os01g0609900'
  24. 'Os01g0654500'
  25. 'Os01g0658400'
  26. 'Os01g0666900'
  27. 'Os01g0905800'
  28. 'Os10g0320400'
  29. 'Os10g0478200'
  30. 'Os10g0167300'
  31. 'Os10g0552600'
  32. 'Os10g0552800'
  33. 'Os10g0569200'
  34. 'Os11g0102200'
  35. 'Os11g0170400'
  36. 'Os11g0220800'
  37. 'Os11g0167800'
  38. 'Os11g0169900'
  39. 'Os11g0199200'
  40. 'Os11g0244800'
  41. 'Os11g0251400'
  42. 'Os11g0414000'
  43. 'Os12g0101800'
  44. 'Os12g0167900'
  45. 'Os12g0428600'
  46. 'Os12g0502200'
  47. 'Os12g0560900'
  48. 'Os12g0278800'
  49. 'Os12g0443700'
  50. 'Os12g0514500'
  51. 'Os12g0561000'
  52. 'Os12g0568200'
  53. 'Os02g0102300'
  54. 'Os02g0105200'
  55. 'Os02g0131300'
  56. 'Os02g0170100'
  57. 'Os02g0175800'
  58. 'Os02g0274100'
  59. 'Os02g0519700'
  60. 'Os02g0519900'
  61. 'Os02g0621700'
  62. 'Os02g0745600'
  63. 'Os02g0785800'
  64. 'Os02g0101700'
  65. 'Os02g0162500'
  66. 'Os02g0200900'
  67. 'Os02g0258200'
  68. 'Os02g0287000'
  69. 'Os02g0480900'
  70. 'Os02g0572400'
  71. 'Os02g0767500'
  72. 'Os02g0787800'
  73. 'Os03g0103100'
  74. 'Os03g0139100'
  75. 'Os03g0154700'
  76. 'Os03g0227000'
  77. 'Os03g0241200'
  78. 'Os03g0273800'
  79. 'Os03g0274000'
  80. 'Os03g0297100'
  81. 'Os03g0351500'
  82. 'Os03g0356700'
  83. 'Os03g0388500'
  84. 'Os03g0390400'
  85. 'Os03g0581800'
  86. 'Os03g0606200'
  87. 'Os03g0712700'
  88. 'Os03g0741100'
  89. 'Os03g0743400'
  90. 'Os03g0758800'
  91. 'Os03g0772800'
  92. 'Os03g0796000'
  93. 'Os03g0804800'
  94. 'Os03g0806900'
  95. 'Os03g0821100'
  96. 'Os03g0136900'
  97. 'Os03g0166000'
  98. 'Os03g0234200'
  99. 'Os03g0248600'
  100. 'Os03g0254700'
  101. 'Os03g0401300'
  102. 'Os03g0407000'
  103. 'Os03g0577000'
  104. 'Os03g0586800'
  105. 'Os03g0695600'
  106. 'Os03g0742900'
  107. 'Os03g0743900'
  108. 'Os03g0794700'
  109. 'Os04g0118400'
  110. 'Os04g0418800'
  111. 'Os04g0449900'
  112. 'Os04g0486600'
  113. 'Os04g0551800'
  114. 'Os04g0584600'
  115. 'Os04g0592400'
  116. 'Os04g0432600'
  117. 'Os04g0566500'
  118. 'Os04g0601700'
  119. 'Os04g0620000'
  120. 'Os04g0660500'
  121. 'Os04g0687100'
  122. 'Os05g0105900'
  123. 'Os05g0114700'
  124. 'Os05g0143500'
  125. 'Os05g0154700'
  126. 'Os05g0160200'
  127. 'Os05g0241200'
  128. 'Os05g0317200'
  129. 'Os05g0418000'
  130. 'Os05g0420600'
  131. 'Os05g0460200'
  132. 'Os05g0481600'
  133. 'Os05g0490100'
  134. 'Os05g0498400'
  135. 'Os05g0533100'
  136. 'Os05g0556900'
  137. 'Os05g0155601'
  138. 'Os05g0160300'
  139. 'Os05g0346300'
  140. 'Os05g0455500'
  141. 'Os05g0477300'
  142. 'Os05g0482700'
  143. 'Os05g0486700'
  144. 'Os05g0503300'
  145. 'Os05g0511400'
  146. 'Os05g0553000'
  147. 'Os05g0587100'
  148. 'Os05g0592600'
  149. 'Os06g0116100'
  150. 'Os06g0336200'
  151. 'Os06g0367100'
  152. 'Os06g0574500'
  153. 'Os06g0646500'
  154. 'Os06g0693200'
  155. 'Os06g0727200'
  156. 'Os06g0728000'
  157. 'Os06g0114000'
  158. 'Os06g0153400'
  159. 'Os06g0208300'
  160. 'Os06g0247500'
  161. 'Os06g0562600'
  162. 'Os06g0568200'
  163. 'Os06g0598900'
  164. 'Os06g0639100'
  165. 'Os06g0701100'
  166. 'Os06g0730600'
  167. 'Os06g0731800'
  168. 'Os07g0176200'
  169. 'Os07g0201100'
  170. 'Os07g0448800'
  171. 'Os07g0577700'
  172. 'Os07g0615200'
  173. 'Os07g0647500'
  174. 'Os07g0675000'
  175. 'Os07g0109500'
  176. 'Os07g0134800'
  177. 'Os07g0202100'
  178. 'Os07g0407700'
  179. 'Os07g0492000'
  180. 'Os07g0495200'
  181. 'Os07g0529800'
  182. 'Os07g0691800'
  183. 'Os08g0113100'
  184. 'Os08g0126300'
  185. 'Os08g0301500'
  186. 'Os08g0314800'
  187. 'Os08g0504700'
  188. 'Os08g0559200'
  189. 'Os08g0117200'
  190. 'Os08g0191100'
  191. 'Os08g0192900'
  192. 'Os08g0295300'
  193. 'Os08g0430500'
  194. 'Os08g0436800'
  195. 'Os08g0478200'
  196. 'Os08g0480100'
  197. 'Os08g0532300'
  198. 'Os09g0361400'
  199. 'Os09g0362800'
  200. 'Os09g0434500'
  201. 'Os09g0484200'
  202. 'Os09g0492700'
  203. 'Os09g0501200'
  204. 'Os09g0509200'
  205. 'Os09g0513000'
  206. 'Os09g0553200'
  207. 'Os09g0556300'
  208. 'Os09g0115400'
  209. 'Os09g0249700'
  210. 'Os09g0258600'
  211. 'Os09g0424300'
  212. 'Os09g0467700'
  213. 'Os09g0469400'
  214. 'Os09g0568800'
In [114]:
# Run GO term analysis with gprofiler2 gost function
cluster_GO <- gost(markers_list3, organism = "osativa", correction_method = "fdr", significant = FALSE, multi_query = FALSE)

cluster_GO_df <- cluster_GO[[1]]

cluster_GO_sig <- filter(cluster_GO_df, p_value<=0.01)
head(cluster_GO_sig, n=5)
A data.frame: 5 × 14
querysignificantp_valueterm_sizequery_sizeintersection_sizeprecisionrecallterm_idsourceterm_nameeffective_domain_sizesource_orderparents
<chr><lgl><dbl><int><int><int><dbl><dbl><chr><chr><chr><int><int><list>
1Atrichoblast_DownTRUE4.609595e-03 4685 70.082352940.15217391KEGG:00999KEGG Biosynthesis of various plant secondary metabolites 3695 162 KEGG:00000
2Atrichoblast_DownTRUE6.360983e-03 3885 60.070588240.15789474KEGG:00460KEGG Cyanoamino acid metabolism 3695 59 KEGG:00000
3Atrichoblast_Up TRUE5.543150e-1212178130.166666670.10743802GO:0009144GO:BPpurine nucleoside triphosphate metabolic process 159483348 GO:0009141
4Atrichoblast_Up TRUE5.543150e-1212078130.166666670.10833333GO:0009205GO:BPpurine ribonucleoside triphosphate metabolic process159483408GO:00091....
5Atrichoblast_Up TRUE1.163328e-1113278130.166666670.09848485GO:0009199GO:BPribonucleoside triphosphate metabolic process 159483402 GO:0009141
In [115]:
## Save the whole GO list
cluster_GO_full_save <- as.matrix (cluster_GO_df)
write.csv(cluster_GO_full_save, file = "./1-DE_analysis/snRNA-seq_CMPvsGel_DE_gene_GO_analysis-full.csv", row.names = TRUE)
In [116]:
# Save the GO term analysis result
cluster_GO_save <- as.matrix (cluster_GO_sig)
write.csv(cluster_GO_save, file = "./1-DE_analysis/snRNA-seq_CMPvsGel_DE_gene_GO_analysis.csv", row.names = TRUE)
In [ ]:

Plot Specific genes for featureplot figures¶

In [117]:
# Read the defense relevant gene list
defense.gene <- read.csv("./1-DE_analysis/Biology_process_genes//Defense_genes.csv")
defense.gene$Gene.ID
  1. 'LOC-Os05g23250'
  2. 'LOC-Os11g44990'
  3. 'LOC-Os07g19320'
  4. 'LOC-Os11g45130'
  5. 'LOC-Os05g34230'
  6. 'LOC-Os11g45090'
  7. 'LOC-Os11g12040'
  8. 'LOC-Os11g44960'
  9. 'LOC-Os11g12330'
  10. 'LOC-Os01g25760'
  11. 'LOC-Os11g45620'
  12. 'LOC-Os11g12000'
  13. 'LOC-Os01g25810'
  14. 'LOC-Os12g10330'
  15. 'LOC-Os08g14850'
  16. 'LOC-Os12g33160'
  17. 'LOC-Os05g34220'
  18. 'LOC-Os12g39620'
  19. 'LOC-Os11g45160'
  20. 'LOC-Os09g10054'
  21. 'LOC-Os07g29810'
  22. 'LOC-Os02g25900'
  23. 'LOC-Os08g07330'
  24. 'LOC-Os12g03080'
  25. 'LOC-Os12g31160'
  26. 'LOC-Os01g71114'
  27. 'LOC-Os06g43670'
  28. 'LOC-Os11g42040'
  29. 'LOC-Os09g14410'
  30. 'LOC-Os01g58530'
In [128]:
# Check Defense relevant genes
DefaultAssay(rc.comparison) <- "SCT"
options(repr.plot.width=12, repr.plot.height=6)
FeaturePlot(rc.comparison, features = "LOC-Os11g45160",
            cols = c("grey", "red"), label=F, repel=F, pt.size = 0.8, 
            label.size = 3.5, order=T, split.by="normal")

Warning message in FeaturePlot(rc.comparison, features = "LOC-Os11g45160", cols = c("grey", :
“All cells have the same value (0) of LOC-Os11g45160.”
In [ ]:

Check the UMI counts¶

In [ ]:
# Check UMI counts in each seurat cluster
options(repr.plot.width=36, repr.plot.height=36)
VlnPlot(object = rc.comparison, features = "nCount_RNA", group.by = "manual.anno")
In [26]:
table(rc.comparison$normal)

  gel  soil 
16219 13838
In [27]:
## Subgroup the "normal" groups for the following analysis
rc.gel <- subset(rc.comparison, cells=colnames(rc.comparison)[which(rc.comparison$normal!="soil")])
In [32]:
# Check UMI counts in each seurat cluster
options(repr.plot.width=12, repr.plot.height=18)
VlnPlot(object = rc.gel, features = "nCount_RNA", group.by = "manual.anno",
        pt.size = 0.1)
In [33]:
## Subgroup the "normal" groups for the following analysis
rc.soil <- subset(rc.comparison, cells=colnames(rc.comparison)[which(rc.comparison$normal!="gel")])
In [43]:
# Check UMI counts in each seurat cluster
options(repr.plot.width=12, repr.plot.height=18)
VlnPlot(object = rc.soil, features = "nCount_RNA", group.by = "manual.anno",
        pt.size = 0.1)
In [35]:
table(rc.integrated$gel_soil)

non-compact soil     compact soil              gel 
           13838            18390            22797
In [36]:
## Subgroup the "normal" groups for the following analysis
rc.cmp <- subset(rc.integrated, cells=colnames(rc.integrated)[which(rc.integrated$gel_soil == "compact soil")])
In [42]:
# Check UMI counts in each seurat cluster
options(repr.plot.width=12, repr.plot.height=18)
VlnPlot(object = rc.cmp, features = "nCount_RNA", group.by = "manual.anno",
        pt.size = 0.1)

Calculate Defense and Vesicle transport gene expressions¶

In [14]:
# Read the defense relevant gene list
defense.gene <- read.csv("./1-DE_analysis/Biology_process_genes//Defense_genes.csv")
defense.gene$Gene.ID
  1. 'LOC-Os05g23250'
  2. 'LOC-Os11g44990'
  3. 'LOC-Os07g19320'
  4. 'LOC-Os11g45130'
  5. 'LOC-Os05g34230'
  6. 'LOC-Os11g45090'
  7. 'LOC-Os11g12040'
  8. 'LOC-Os11g44960'
  9. 'LOC-Os11g12330'
  10. 'LOC-Os01g25760'
  11. 'LOC-Os11g45620'
  12. 'LOC-Os11g12000'
  13. 'LOC-Os01g25810'
  14. 'LOC-Os12g10330'
  15. 'LOC-Os08g14850'
  16. 'LOC-Os12g33160'
  17. 'LOC-Os05g34220'
  18. 'LOC-Os12g39620'
  19. 'LOC-Os11g45160'
  20. 'LOC-Os09g10054'
  21. 'LOC-Os07g29810'
  22. 'LOC-Os02g25900'
  23. 'LOC-Os08g07330'
  24. 'LOC-Os12g03080'
  25. 'LOC-Os12g31160'
  26. 'LOC-Os01g71114'
  27. 'LOC-Os06g43670'
  28. 'LOC-Os11g42040'
  29. 'LOC-Os09g14410'
  30. 'LOC-Os01g58530'
In [15]:
## Check gene existence in single cell data-exodermis
match(defense.gene$Gene.ID,rownames(rc.exodermis@assays$SCT@data))
  1. 19579
  2. 6222
  3. 24075
  4. 6225
  5. 19817
  6. 6224
  7. 5728
  8. 6220
  9. 5733
  10. 2653
  11. 7069
  12. 5727
  13. 2654
  14. 8195
  15. 25069
  16. 8475
  17. 18655
  18. 7801
  19. 6226
  20. 30123
  21. 23146
  22. 9391
  23. 24910
  24. 7996
  25. 8426
  26. 3828
  27. 21191
  28. 7010
  29. 27608
  30. 1480
In [ ]:
In [16]:
# Read the vesicle-mediated transport relevant gene list
transport.gene <- read.csv("./1-DE_analysis/Biology_process_genes//Transport_genes.csv")
transport.gene$Gene.ID
  1. 'LOC-Os01g67810'
  2. 'LOC-Os11g24560'
  3. 'LOC-Os04g04020'
  4. 'LOC-Os02g46510'
  5. 'LOC-Os12g13590'
  6. 'LOC-Os06g07780'
  7. 'LOC-Os06g05804'
  8. 'LOC-Os02g56110'
  9. 'LOC-Os01g32880'
  10. 'LOC-Os05g31780'
  11. 'LOC-Os06g51510'
  12. 'LOC-Os02g24134'
  13. 'LOC-Os12g44250'
  14. 'LOC-Os05g37120'
  15. 'LOC-Os03g53140'
  16. 'LOC-Os11g36400'
  17. 'LOC-Os06g07090'
  18. 'LOC-Os05g47550'
  19. 'LOC-Os02g55970'
  20. 'LOC-Os08g13270'
  21. 'LOC-Os03g42320'
  22. 'LOC-Os04g46079'
  23. 'LOC-Os03g02150'
  24. 'LOC-Os11g42989'
  25. 'LOC-Os09g04110'
  26. 'LOC-Os05g30640'
  27. 'LOC-Os09g36976'
  28. 'LOC-Os01g08400'
  29. 'LOC-Os02g35640'
  30. 'LOC-Os01g24950'
  31. 'LOC-Os06g40630'
  32. 'LOC-Os01g55799'
  33. 'LOC-Os01g67820'
  34. 'LOC-Os08g35470'
  35. 'LOC-Os03g50350'
  36. 'LOC-Os01g17430'
  37. 'LOC-Os02g25580'
  38. 'LOC-Os07g07000'
  39. 'LOC-Os07g14540'
  40. 'LOC-Os05g39610'
  41. 'LOC-Os02g11830'
  42. 'LOC-Os04g13470'
  43. 'LOC-Os12g24250'
  44. 'LOC-Os10g20240'
  45. 'LOC-Os03g58840'
  46. 'LOC-Os08g14640'
  47. 'LOC-Os04g58880'
  48. 'LOC-Os06g19620'
  49. 'LOC-Os05g02140'
  50. 'LOC-Os04g31330'
  51. 'LOC-Os03g16800'
  52. 'LOC-Os12g35360'
  53. 'LOC-Os06g07830'
  54. 'LOC-Os03g50300'
  55. 'LOC-Os01g50010'
  56. 'LOC-Os01g42830'
  57. 'LOC-Os01g69230'
  58. 'LOC-Os07g49300'
  59. 'LOC-Os02g11840'
  60. 'LOC-Os03g50340'
  61. 'LOC-Os03g20670'
  62. 'LOC-Os01g21850'
  63. 'LOC-Os02g43590'
  64. 'LOC-Os06g09850'
  65. 'LOC-Os04g52270'
  66. 'LOC-Os03g57760'
  67. 'LOC-Os10g33630'
  68. 'LOC-Os06g02570'
  69. 'LOC-Os11g07280'
  70. 'LOC-Os11g06740'
In [17]:
## Check gene existence in single cell data
match(transport.gene$Gene.ID,rownames(rc.exodermis@assays$SCT@data))
  1. 1791
  2. 5855
  3. 15582
  4. 9907
  5. 8234
  6. 21663
  7. 21602
  8. 11871
  9. 743
  10. 19746
  11. 22622
  12. 10978
  13. 7923
  14. 19885
  15. 13402
  16. 6913
  17. 20528
  18. 20170
  19. 10251
  20. 25033
  21. 14852
  22. 17512
  23. 12023
  24. 6177
  25. 27477
  26. 18550
  27. 28121
  28. 239
  29. 11205
  30. 629
  31. 21127
  32. 1373
  33. 1792
  34. 25418
  35. 15070
  36. 2518
  37. 10991
  38. 23888
  39. 22942
  40. 19961
  41. 10725
  42. 15665
  43. 8358
  44. 4145
  45. 13602
  46. 26032
  47. 17983
  48. 21945
  49. 19215
  50. 15855
  51. 14328
  52. 8513
  53. 21665
  54. 13301
  55. 1173
  56. 958
  57. 1836
  58. 23747
  59. 10726
  60. 15069
  61. 12722
  62. 2592
  63. 11440
  64. 21726
  65. 17722
  66. 15299
  67. 4373
  68. 21495
  69. 6491
  70. 5637
In [ ]:

Start to collect the mean value for gene expressions in SCT¶

In [179]:
# Check DE gene expression-defense
DefaultAssay(rc.comparison) <- "SCT"
options(repr.plot.width=12, repr.plot.height=6)
FeaturePlot(rc.comparison, features = "LOC-Os07g14540",
            cols = c("grey", "red"), label=F, repel=F, pt.size = 0.8, 
            label.size = 3.5, order=T, split.by="condition")
In [ ]:
In [ ]:
# Check the Trichoblast markers-Correlation analysis
options(repr.plot.width=18, repr.plot.height=42)
DefaultAssay(rc.integrated) <- "SCT"
FeaturePlot(rc.integrated, cols = c("grey", "#Ff4061"), 
            feature = c("LOC-Os07g01420","LOC-Os01g07060",
                        "LOC-Os05g38770","LOC-Os06g08500","LOC-Os01g11750",
                        "LOC-Os01g07030","LOC-Os06g01920","LOC-Os07g30090",
                        "LOC-Os04g46910","LOC-Os07g26460","LOC-Os12g05380",
                        "LOC-Os02g18430","LOC-Os07g01420","LOC-Os07g30090",
                        "LOC-Os05g35810","LOC-Os01g18970","LOC-Os06g02390",
                        "LOC-Os01g13120","LOC-Os03g04210","LOC-Os02g17880"), 
            order = T, ncol = 3)
In [ ]:
In [ ]:
In [4]:
# Check all the packages versions
sessionInfo()

R version 4.2.0 (2022-04-22)
Platform: x86_64-conda-linux-gnu (64-bit)
Running under: CentOS Stream 8

Matrix products: default
BLAS/LAPACK: /hpc/group/pbenfeylab/mz187/miniconda3/envs/muscat/lib/libopenblasp-r0.3.21.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats4    grid      stats     graphics  grDevices utils     datasets 
[8] methods   base     

other attached packages:
 [1] future_1.32.0               scran_1.26.0               
 [3] scuttle_1.8.0               SingleCellExperiment_1.20.0
 [5] SummarizedExperiment_1.28.0 Biobase_2.58.0             
 [7] GenomicRanges_1.50.0        GenomeInfoDb_1.34.9        
 [9] IRanges_2.32.0              S4Vectors_0.36.0           
[11] BiocGenerics_0.44.0         MatrixGenerics_1.10.0      
[13] matrixStats_1.0.0           limma_3.54.0               
[15] muscat_1.12.0               ggrepel_0.9.3              
[17] gprofiler2_0.2.2            GeneOverlap_1.34.0         
[19] circlize_0.4.15             ComplexHeatmap_2.14.0      
[21] cowplot_1.1.1               Seurat_3.1.5               
[23] lubridate_1.9.2             forcats_1.0.0              
[25] stringr_1.5.0               dplyr_1.1.2                
[27] purrr_1.0.1                 readr_2.1.4                
[29] tidyr_1.3.0                 tibble_3.2.1               
[31] ggplot2_3.4.2               tidyverse_2.0.0            

loaded via a namespace (and not attached):
  [1] utf8_1.2.3                reticulate_1.25          
  [3] tidyselect_1.2.0          lme4_1.1-33              
  [5] RSQLite_2.3.1             AnnotationDbi_1.60.0     
  [7] htmlwidgets_1.6.2         BiocParallel_1.32.5      
  [9] Rtsne_0.16                ScaledMatrix_1.6.0       
 [11] munsell_0.5.0             codetools_0.2-19         
 [13] ica_1.0-3                 statmod_1.4.36           
 [15] pbdZMQ_0.3-9              withr_2.5.0              
 [17] colorspace_2.1-0          uuid_1.1-0               
 [19] ROCR_1.0-11               listenv_0.9.0            
 [21] Rdpack_2.4                repr_1.1.6               
 [23] GenomeInfoDbData_1.2.9    bit64_4.0.5              
 [25] glmmTMB_1.1.7             parallelly_1.36.0        
 [27] vctrs_0.6.3               generics_0.1.3           
 [29] timechange_0.2.0          R6_2.5.1                 
 [31] doParallel_1.0.17         ggbeeswarm_0.7.2         
 [33] clue_0.3-64               rsvd_1.0.5               
 [35] locfit_1.5-9.8            bitops_1.0-7             
 [37] cachem_1.0.8              DelayedArray_0.24.0      
 [39] scales_1.2.1              beeswarm_0.4.0           
 [41] gtable_0.3.3              beachmat_2.14.0          
 [43] globals_0.16.2            rlang_1.1.1              
 [45] genefilter_1.80.0         GlobalOptions_0.1.2      
 [47] splines_4.2.0             TMB_1.9.4                
 [49] lazyeval_0.2.2            broom_1.0.5              
 [51] reshape2_1.4.4            backports_1.4.1          
 [53] tools_4.2.0               gplots_3.1.3             
 [55] RColorBrewer_1.1-3        ggridges_0.5.4           
 [57] Rcpp_1.0.10               plyr_1.8.8               
 [59] base64enc_0.1-3           sparseMatrixStats_1.10.0 
 [61] progress_1.2.2            zlibbioc_1.44.0          
 [63] RCurl_1.98-1.12           prettyunits_1.1.1        
 [65] viridis_0.6.3             pbapply_1.7-0            
 [67] GetoptLong_1.0.5          zoo_1.8-12               
 [69] cluster_2.1.4             variancePartition_1.28.0 
 [71] magrittr_2.0.3            data.table_1.14.8        
 [73] lmerTest_3.1-3            lmtest_0.9-40            
 [75] RANN_2.6.1                fitdistrplus_1.1-11      
 [77] hms_1.1.3                 patchwork_1.1.2          
 [79] evaluate_0.21             xtable_1.8-4             
 [81] pbkrtest_0.5.2            RhpcBLASctl_0.23-42      
 [83] XML_3.99-0.9              gridExtra_2.3            
 [85] shape_1.4.6               compiler_4.2.0           
 [87] scater_1.26.0             KernSmooth_2.23-21       
 [89] crayon_1.5.2              minqa_1.2.5              
 [91] htmltools_0.5.5           tzdb_0.4.0               
 [93] geneplotter_1.76.0        DBI_1.1.3                
 [95] MASS_7.3-60               boot_1.3-28.1            
 [97] Matrix_1.5-4.1            cli_3.6.1                
 [99] rbibutils_2.2.13          metapod_1.6.0            
[101] parallel_4.2.0            igraph_1.5.0             
[103] pkgconfig_2.0.3           numDeriv_2016.8-1.1      
[105] IRdisplay_1.1             plotly_4.10.0            
[107] foreach_1.5.2             annotate_1.76.0          
[109] vipor_0.4.5               dqrng_0.3.0              
[111] blme_1.0-5                XVector_0.38.0           
[113] digest_0.6.31             sctransform_0.3.5        
[115] RcppAnnoy_0.0.20          tsne_0.1-3.1             
[117] Biostrings_2.66.0         leiden_0.4.3             
[119] uwot_0.1.14               edgeR_3.40.0             
[121] DelayedMatrixStats_1.20.0 gtools_3.9.4             
[123] rjson_0.2.21              nloptr_2.0.3             
[125] lifecycle_1.0.3           nlme_3.1-157             
[127] jsonlite_1.8.5            aod_1.3.2                
[129] BiocNeighbors_1.16.0      viridisLite_0.4.2        
[131] fansi_1.0.4               pillar_1.9.0             
[133] lattice_0.21-8            KEGGREST_1.38.0          
[135] fastmap_1.1.1             httr_1.4.6               
[137] survival_3.5-5            glue_1.6.2               
[139] png_0.1-8                 iterators_1.0.14         
[141] bluster_1.8.0             bit_4.0.5                
[143] stringi_1.7.6             blob_1.2.4               
[145] BiocSingular_1.14.0       DESeq2_1.38.0            
[147] caTools_1.18.2            memoise_2.0.1            
[149] IRkernel_1.3.2            irlba_2.3.5.1            
[151] future.apply_1.11.0       ape_5.7-1